Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Trouble with Two Stage Longitudinal Analysis
by Timothy Hendrickson 23 Nov '16

23 Nov '16

FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the problem is a mismatch. I am wondering if I made some sort of mistake in my script design or design matrix creation... Anyway here is the command line input: mri_glmfit --glmdir lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y lh.testretest.thickness-pc1.stack.fwhm10.mgh --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx --label lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error
by Jennifer Barredo 23 Nov '16

23 Nov '16

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead file transfer protocols for a patch for mri_convert that might solve my problem. May I please have a patch for mri_convert? I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and OSX Yosemite. Thank you, Jennifer -- Jennifer Barredo, PhD Staff Scientist Providence VA Medical Center Research Affiliate Brown Institute for Brain Sciences jlbarredo(a)gmail.com Jennifer.Barredo(a)va.gov

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Freeview -dti Display as Vectors Discrepancy
by Douglas Merkitch 23 Nov '16

23 Nov '16

Hello experts, I have come across what I think could be an inconsistency with how freeview interprets and/or displays dti data as vectors. Specifically, the x component seems to be inverted in freeview from freesurfer-Darwin-lion-stable-pub-v5.3.0 as compared to fslview (version 509) AND freeview from freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae. Is this a known issue with a patch available? Any insight would be greatly appreciated. Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters
by Antonin Skoch 23 Nov '16

23 Nov '16

Dear Martin, thank you for the explanations, and sorry, I missed your previous response. Just I am wondering, what is the reason of the shrinkage? Why not to start directly from pial surface of the base? And, I also found a binary mris_longitudinal_surfaces, which is, however, not used in recon-all. What is the significance of this binary? Antonin ------------------------------- Hi Antonin, max does not constrain thickness. The location of the max is constrained to be within 2*max for every iteration, so it will constrain how far outwards it searches. But it will be done at each scale, so it can still deform a long way. We initialize the surface processing in long with the surface from the base. But we don’t use the pial from base directly, instead we shrink it a little first and start from there. Not sure about the last question (difference between orig and prig-white parameters). Best, Martin > On Nov 14, 2016, at 10:17 PM, Antonin Skoch <ansk at ikem.cz> wrote: > > Dear experts, > > I am trying to understand how the pial and white surfaces are generated in longitudinal stream using information from the reconstructed base template (freeSurfer development version). > > In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also parameters -long and -max 3.5. > > May I ask what is the significance of these parameters? > > -max 3.5 means constraining cortical thickness to 3.5 mm? Why this constraint is applied specifically in longitudinal stream? > > In mris_make_surfaces.c I found that -long means that initial pial vertex positions are set between final white and orig pial, slightly inside orig_pial. What is the significance of this setting in longitudinal stream? > > Last question, not related specifically to longitudinal stream: What is the difference between -orig and -orig_white parameters of mris_make_surfaces? From the reading of source codes (quite tough to me) I got an impression that from -orig the gray and white matter histogram values are computed whereas -orig_white defines initial position of the vertices in the first iteration (which, for some reasons, does not necessary has to be identical to -orig). Am I correct? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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Freesurfer November 2016