Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

a question on flat surface
by peng 10 May '14

10 May '14

Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page: http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change. Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong. Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours. btw: the inflated surface is OK either checked by freeview or matlab. best Peng

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Re: [Freesurfer] Viewing functional data on the inflated brain
by Sherryse Corrow 09 May '14

09 May '14

Thanks Douglas. Yes, both of those exist. -- Sherryse Corrow, Ph.D. / Postdotoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org On 5/7/14, 6:54 P, "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.du> wrote: >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.mghharvard.edu/mailman/listinfo/freesurfer >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: Viewing functional data on the inflated brain > (Sherryse Corrow) > 2. Re: vertex-wise cortical thickness and whole brain labeling > (Douglas N Greve) > 3. Re: Question about Qdec p-values (Douglas N Greve) > 4. Re: Quesion about lobar volumes (Douglas N Greve) > 5. Re: Viewing functional data on the inflated brain > (Douglas N Greve) > 6. Re: vertex-wie cortical thickness and whole brain labeling > (Bruce Fischl) > 7. Re: aseg.stats volume mismatch (Gabor Perlaki) > 8. Re: aseg.stats volume mismatch (Bruce Fischl) > 9. Covert processed RS time series to MNI152 (Paul Beach) > 10. Re: Quesion about lobar volume (pfotiad(a)nmr.mgh.harvard.edu) > 11. Re: Quesion about lobar volumes (Douglas N Greve) > 12. Re: Quesion about lobar volumes (pfotiad(a)nmr.mgh.harvard.edu) > 13. Re: LOOK FOR HELP! (???) > > >-------------------------------------------------------------------- > >Message: 1 >Date: Wed, 7 May 2014 10:59:55 -0700 >From: Sheryse Corrow <sherryse.corrow(a)eyecarecentre.org> >Subject: Re: [Freesurfer] Viewing functional data on the inflated > brain >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>>Message-ID: <CF8FC0ED.AE9A%sherryse.corrow(a)eyecarecentre.org> >Content-Type: text/plain; charset="windows-1252" > >Tanks Douglas. We tried that . . . The registration matrix that we need >is not created. Here is the output log file (attache). I am a bit new to >this so I am hoping it has the information you need. After taking a quick >glance at the log file, we noticed there are errors in the log file. > >Step by step, this is what we did after we an recon-all: >Reg-feat2anat ?feat OurFeatDirectory.feat ?subject P209 > >When we open the folder experiment.feat/reg/freesurfer, there is no >anat2exf.register.dat file. However, there is a file called: >anat2exf.register.dat.init. > >Thanks, >Sherryse >-- >Sherryse Corrow, Ph.D. / Postdoctoral Fellow >Human Vision and Eye Movement Lab >Department of Ophthalmoogy & Visual Sciences >UBC/VGH Eye Care Centre >360A-2550 Willow Street >Vancouver, BC, V5Z 3N9 >Tel: 604-875-4111 ext 67672 > >Cell: 604-315-6717 > >sherryse.corrow(a)eyecarecentre.org > > > > > >On 5/6/14, 9:00 AM, "freesurfer-request(a)nmr.mgh.harvard.edu" ><freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > >>Re: Viewing functional data on the inflated brain > >

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nonlinear models in longitudinal analysis
by Jodie Davies-Thompson 09 May '14

09 May '14

Dear Freesurfer experts, I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to 3. However, I am primarily interested in finding regions which show a) an increase between timepoint 1 and 2, but no difference between 2 and 3, and b) no difference between timepoint 1 and 2, but an increase between 2 and 3. Would the correct way of 'modelling' these two in the qdec file be: a) fsid fsid-base years day1 base 0 day2 base 3 day3 base 3 and b) fsid fsid-base years day1 base 0 day2 base 0 day3 base 3 All the best, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003

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Covert processed RS time series to MNI152
by Paul Beach 09 May '14

09 May '14

Hi Freesurfers, I have several processed resting time series files (processed through AFNI) and I'd like to convert them to MNI space. I have done this successfully for T1Volumes and some ROI masks using mri_convert and tried to use the same code for the resting series. However, I've run into a few issues - namely that the transformation cuts off part of the top of the cortex. My code: *mri_convert -it nii -ot mgz CleanData_RestState.nii.gz CleanData_RestState.mgz* *mri_convert CleanData_RestState.mgz --apply_transform transforms/talairach.xfm \* *-oc 0 0 0 CleanData_RestState_talairach.mgz * *mri_convert CleanData_RestState_talairach.mgz \ cleanData_RestState_talairach.nii.gz* The final time series file, overlayed on the transformed T1Volume, is below. [image: Inline image 1] Any suggestions? How big a problem is this? Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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Freesurfer-Tracula Error
by Elia S. 09 May '14

09 May '14

Dear Freesurfer Staff, I encountered the following error while running tracula - longitudinal: ERROR: flag ; unrecognized The exact command line i ran is the following one: trac-all -prep -c '/home/elia/scripts/Tracula/LCL/dcmTimePoints_tar-2/tracula.config' I will attach the complete error log as well as my dmrirc file (which I called in this case tracula.config). Best,Elia -------------------------------------------------------------------------------------------------------------- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux My Current Working Directory: /home/elia

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flash v.s. mprage
by Gregory Kirk 09 May '14

09 May '14

looking at the docs available it seems that in general flash is prefered but it seems that for cortical thickness studies you may still favor the mprage ? all with good parameter setting of course. thanks in advance for any clarifying comments you may have Greg

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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
by Emil H.J. Nijhuis 09 May '14

09 May '14

Dear Bruce, thank you for your help. attached I have put an fslview, tkmedit screen-shot of the T2 image and a tksurfer image of lh.woT2.pial. It appears that without consideration of the T2 this effect does not happen. What would be your recommendation if I would like to keep using the T2 weighted image? Yours, Emil Hi Emil how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1? cheers Bruce On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: Hi, I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue. The command line I have used was: recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T Are you familiar with this issue and do you have some advice for me? Thank you very much for your help. Yours sincerely, Emil -- ---------------------------------------------- Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Information on automatic segmentation method
by dorothee schoemaker 08 May '14

08 May '14

Hi, >From what I understand, Freesurfer's automatic segmentation pipeline is partly based on a training set of subjects manually segmented. Is there a way to get more information on which protocol/guideline was used to manually segment (or define anatomical boundaries) these subjects at the baseline? I am unable to find this information... Thank you in advance for your assistance! Dorothée. -- *PhD candidate in Clinical Psychology* *McGill University* *McGill Centre for Studies in Aging* *Montreal, CANADA*

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Information on automatic segmentation method
by Dorothee Schoemaker 08 May '14

08 May '14

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problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
by Emil H.J. Nijhuis 08 May '14

08 May '14

Hi, I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue. The command line I have used was: recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T Are you familiar with this issue and do you have some advice for me? Thank you very much for your help. Yours sincerely, Emil -- ---------------------------------------------- Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland

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