Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Re: [Freesurfer] Adding control points to aparc+aseg
by Nicholas Goh 13 Nov '17

13 Nov '17

I have still been having trouble with fixing the white matter of the aparc+aseg.mgz file for a subject. I have tried using recon-all -autorecon2-cp -autorecon3 -subjid XXXX recon-all -autorecon2-wm -subjid XXXX recon-all -autorecon2-wm -autorecon3 -subjid XXXX None of these have solved the issue, and I was hoping for help in finding a way to fix this? There are other more extreme examples, but this one seems to have an error at [-7, 114, 133] Thank you for the help, Nicholas Goh On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh <ngoh95(a)gmail.com> wrote: > Ping, is this okay to do? I Think it is but wanted to check before sending > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Thu, Sep 28, 2017 at 5:23 PM > Subject: Re: [Freesurfer] Adding control points to aparc+aseg > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > > Hi Nicholas > > why don't you tar, gzip and upload your subject and we will take a look. > Make sure to tell us the coordinates of where you are trying to fix things > > cheers > Bruce > > > On Thu, 28 Sep 2017, Nicholas Goh wrote: > > I am still having trouble with getting the aparc+aseg to recognize sections >> that should be white matter as such. Using the control points paired >> withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX >> >> did not work, after 4 or 5 attempts with different control points, and >> using >> recon-all -autorecon2-wm -s XXXX >> also did not yield appreciable results. Is there anything else that I >> might >> be able to try to fix this? >> Thank you for all the help, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak <fkm24(a)medschl.cam.ac.uk> >> wrote: >> Hi Nicholas, >> >> In such situations, I have learned that autorecon2-wm after adding WM >> voxels seems to work pretty well. Hope that helps. >> >> Best Wishes, >> Elijah >> >> On 27 September 2017 at 16:46:43, Nicholas Goh (ngoh95(a)gmail.com) >> wrote: >> >> Bruce, >> Thank you for the response. Attempting to use this method has >> not produced results, and I am unsure how to proceed or if I had >> performed it improperly. I have attached an example of the >> control points being placed, if that helps any. >> Thank you, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Nicholas >> >> yes, possibly, depending on why you are missing >> chunks. If the white matter in the regions you are >> missing has intensity values significantly < 110 >> then what you are doing should help. The control.dat >> file must be place in the subject/tmp dir for us to >> find it. >> >> cheers >> Bruce >> On Wed, 27 Sep 2017, Nicholas Goh wrote: >> >> I am attempting to fix the >> aparc+aseg.mgz file for an image, and >> wanted to check to see if I am >> doing it correctly.What I was doing >> which seemed to be ineffective was >> 1)create a new point set of control >> points labelled control.dat >> 2)place control points along what should >> be white matter >> 3)save point set >> 4)run recon-all -autorecon2-cp >> -autorecon3 -subjid XXXX >> >> Is this the correct way to go about >> fixing aparc+aseg files that are missing >> chunks of the brain? Is >> there a better way to go about this? >> Thanks for the help, >> >> Nicholas Goh >> >> >> _______________________________________________ >> 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 >> >> >> 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. > > >

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Registration
by N Saf 08 Nov '17

08 Nov '17

Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ? thank's alot for your great support. BRG, Nazanin

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Qdec result
by hiroki.sato＠med.tohoku.ac.jp 07 Nov '17

07 Nov '17

Dear experts I'm using Qdec. I want to check regions where age and thickness are correlated, and regions where the thickness-age correlation differ between genotype(Hetero or WT). When I choose "genotype(Hetero or WT)" as Fixed factors and "age" as Continuous variables, I can choice the results "Does the correlation between thickness and age, accounding for genotype, differ from zero" and "Does the thickness-age correlation differ between Hetero and WT?". I have two questions. Is "Does the correlation between thickness and age, accounding for genotype, differ from zero" equal to the results of "Does the correlation between thickness and age differ from zero" that I choose only "age" as Continuous variables? I don't know the meaning of "accounding for genotype" but these two results are almost same. Does just a little different results come from the difference of Degrees Of Freedom? Thank you in advance. Best, Hiroki

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missing register.dof6.dat
by Guy Avraham 07 Nov '17

07 Nov '17

Hello Freesurfer developers, I was running FSFAST preprocessing: preproc-sess -s [subject] -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 0 -per-run The process finished without errors. However, the register.dof6.dat is missing from the subject's folder. I could not find any error in the register.dof6.dat.log file (see attached). - Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - OS: Ubuntu 16.04 LTS - recon-all.log file is also attached. Thanks! Guy

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mri_cvs_register: how to read/import .m3z warp file
by Stefano Zappalà 06 Nov '17

06 Nov '17

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler file format to convert the warp field to. No information about it seems to be reported in the website. Moreover, I've searched the list and a similar question was not answered. I was wondering if you have some suggestions in reading the output warp field of mri_cvs_register. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04 LTS Many thanks, Stefano.

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significant of long_mris_slopes
by lanbo Wang 01 Nov '17

01 Nov '17

Dear freesurfer group, Hi! I used long_stats_slopes and code to process my longitudinal data: long_stats_slopes --qdec sub_qdec_long.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-rate --generic-time --stack-rate thickness.lh.aparc-rate.stack.txt mri_glmfit --osgm --glmdir thickness.lh.aparc-rate --table thickness.lh.aparc-rate.stack.txt I got results sig.table.dat in folder of 'thickness.lh.aparc-rate'. I want to ask what's meaning of this results. Is it the significant results or just directly result? All best, Lanbo Wang

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Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error
by Patricia Linortner 01 Nov '17

01 Nov '17

Hi all, I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B: -hippocampal-subfields-T1T2). For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial brain). Segmentation works in most subjects, but in some subjects the co-registration of the 7T-T2 MRI scan fails. [Despite good scan quality and pre-alignment using Freeview] I was wondering if you had any input/suggestion(s) for fixing this error (e.g. using mri_register)? Thanks, Patricia

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Re: [Freesurfer] Occiptial flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

Yes the lh.occip.patch.3d is in the surf folder for each subject.

2 1

Occipital flattening
by Patricia Stefancin 31 Oct '17

31 Oct '17

In response to my previous question, the command line I was using was mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat When I run this, the terminal output reads : lh.occip.patch.3d no such file or directory. I followed all the steps to create the patch, and saved the file with tksurfer. I don't know what could be going on.

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Using Freesurfer Recon1 with Brainvoyager QX
by Ashley A Presley 31 Oct '17

31 Oct '17

Hello, I am trying to use the skullstripping process of recon 1 to clean up the brains before importing into Brainvoyager QX. I convert the files to nifti in freesurfer then to VMR in Brainvoyager with the nifti gifti plugin. When I do this, however, the brain appears to be rotated and using Brainvoyager's manual spacial transformation makes the problem worse. I've attached a screenshot of the brainvoyager window after importing it through nifti gifti. Specs if needed: System: ubuntu 16.04 LTS Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c [cid:3FB7919ECFAE4272A3D7C63E5E71A258] NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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Freesurfer October 2017