Freesurfer

freesurfer@nmr.mgh.harvard.edu

9 participants
30092 discussions

Re: [Freesurfer] editing topological defect
by Antonin Skoch 28 Feb '17

28 Feb '17

Dear Shane, the "topological defect" in FreeSurfer jargon means that the estimated surface contains errors like "holes" or "handles". See PPT from FreeSurfer course http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt or https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData XL (=extra large?) defect often means large error in previous steps of recon-all, usually skullstrip or white matte segmentation. In some cases the error is automatically corrected, but not always. To see, what is happening, I would suggest to inspect brainmask.mgz or wm.mgz and correct errors. You can also find more information on the forum, there are quite large amount of posts related to topological defects. For example: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30763.html Antonin Skoch Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane

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XL defect detected
by Shane Schofield 28 Feb '17

28 Feb '17

Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane -- Shane Schofield

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wm editting doubt
by Manuel Delgado 28 Feb '17

28 Feb '17

Hello all, I have a basic question regarding the wm edition. As you can see in the images attached, the white matter mask includes the ventricle in one side but excludes it in the other. My question is: do I have to draw the voxels that are excluded from the white matter mask? I apologize if this issue has been previously raised. Best, Manuel

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Re: [Freesurfer] ACPC alignment before or after running on Freesurfer?
by Antonin Skoch 28 Feb '17

28 Feb '17

Dear Kristine, I am currently experimenting with prepending PreFreeSurferPipeline.sh to recon-all (of HCP pipelines https://github.com/Washington-University/Pipelines ) which does APCP alignment, robust FOV (cropping of unrelevant parts of image FOV - neck etc.), bias correction and (optionally) FNIRT-based skullstrip and gradient nonlinearity correction. I believe that ACPC alignment could prevent Talairach registration errors/inaccuracies in recon-all which could have profound effect on subsequent skullstrip and subcortical labeling (it could at least prevent to disastrous errors which some other users reported recently, such as this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51789.html) This could also help to mutual registration of data of multiple sessions (i.e. in longitudinal studies) to compensate different head positioning. It could be also beneficial to use FNIRT-based skullstrip to help (or even to replace) freesurfer's skullstrip (as is it done in FreeSurferPipeline.sh of HCP pipelines), since, to my experience, the inaccurate skullstrip is basis of most errors in FreeSurfer reconstruction stream. This FNIRT skullstrip works fine with our high-quality data from 64-channel coil acquired by protocol similar to Human connectome project (I ocasionally find only several, probably negligible amount of voxels of gray matter cut-out), but not as good with older data where significant parts of gray matter are often cut-out. The drawback is that when you want to get to the original space, you have to account one more transformation and there is one more step in processing pipeline you need to check. This is my view based on current experience. I would also greatly appreciate any comment (different perspective) of other users. Regards, Antonin Dear Freesurfer team, This may sound like a bit of a small question, but I could not find any exact answer elsewhere.Does the exact orientation of the input image have much effect on the accuracy of the segmentation in Freesurfer? It seems that some people apply ACPC alignment to the output of Freesurfer, so I am confused as to which order would be optimal. Thank you in advance, Kristine

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Re: [Freesurfer] gzip: stdin: unexpected end of file
by Kambiz Tavabi 27 Feb '17

27 Feb '17

sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz returns da39a3ee5e6b4b0d3255bfef95601890afd80709 A corrupted download three times! Do I just try downloading again? On Thu, Feb 23, 2017 at 9:02 AM <freesurfer-request(a)nmr.mgh.harvard.edu> 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.mgh.harvard.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. No FTP Access (Rockers, Elijah D.) > 2. Re: No FTP Access (Rockers, Elijah D.) > 3. Re: gzip: stdin: unexpected end of file (Z K) > 4. Re: Re-running after Base Image Edits (Steros) > 5. Re: FS 6.0 Freeview (peng) > 6. Re: FS 6.0 Freeview (Kevin Aquino) > 7. Virtualbox for FS v6.0 ? (Randolph Andrews) > 8. recon-all error (6.0) (Trisanna Sprung-Much) > 9. deformation fields (Worker, Amanda) > 10. How to output particular area from stats subdir (Jing Gu) > > > > ---------- Forwarded message ---------- > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Wed, 22 Feb 2017 17:22:06 +0000 > Subject: [Freesurfer] No FTP Access > Is there by any chance another way to download Freesurfer? My > institution does not allow FTP connections (HIPPA...) Same goes for the > tutorial data, but obviously Freesurfer is the priority here... thanks. > > - Eli > > Houston Methodist. Leading Medicine. > > U.S. News & World Report has recognized Houston Methodist as one of the > nation’s top 20 hospitals, placing it for the second time on the magazine’s > prestigious Honor Roll. It is also designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > > > ---------- Forwarded message ---------- > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Wed, 22 Feb 2017 17:24:23 +0000 > Subject: Re: [Freesurfer] No FTP Access > Nevermind. I discovered if I just change ftp to https in the download > link, it works fine. > - Eli > > On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote: > > Is there by any chance another way to download Freesurfer? My > > institution does not allow FTP connections (HIPPA...) Same goes for the > > tutorial data, but obviously Freesurfer is the priority here... thanks. > > > > - Eli > > > Houston Methodist. Leading Medicine. > > U.S. News & World Report has recognized Houston Methodist as one of the > nation’s top 20 hospitals, placing it for the second time on the magazine’s > prestigious Honor Roll. It is also designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > > > ---------- Forwarded message ---------- > From: Z K <zkaufman(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: > Bcc: > Date: Wed, 22 Feb 2017 12:54:38 -0500 > Subject: Re: [Freesurfer] gzip: stdin: unexpected end of file > Its probably a corrupted download. What do you get when type 'sha1sum > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz'? > > $> sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > 1723ef916c4e74ee8fff72438e9c6c91c79bd4cb > > You should get the 1723ef... number from above. > > On 02/21/2017 07:27 PM, Kambiz Tavabi wrote: > > > > After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt > > 16.04 (64b) machine with > > > > tar -C /usr/local -xzvf > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > > > Returns an error: > > gzip: stdin: unexpected end of file > > tar: Child returned status 1 > > tar: Error is not recoverable: exiting now > > > > Is there a way around this? > > > > > > ------------------------------------------------------------ > > Kambiz Tavabi PhD > > Institute for Learning & Brain Sciences > > 1715 Columbia Road N > > Portage Bay Building > > Box 357988 > > University of Washington > > Seattle, WA 98195-7988 > > Tel: 206-685-6173 <(206)%20685-6173> > > ------------------------------------------------------------ > > > > /Confidentiality Notice: Because email is not secure, please be aware > > that we cannot guarantee the confidentiality of information sent by > > email. If you are not the intended recipient of this email, please > > notify the sender by reply email, and then destroy all copies of the > > message and any attachments./ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ---------- Forwarded message ---------- > From: Steros <steros(a)nmr.mgh.harvard.edu> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Wed, 22 Feb 2017 12:08:40 -0800 > Subject: Re: [Freesurfer] Re-running after Base Image Edits > Hello Corrina, > > I believe the answer to your question is Pho. > > Best, > Stephanie > > On Feb 21, 2017, at 5:22 PM, Corrina Fonseca <cosfonse(a)gmail.com> wrote: > > Hi there, > > We are attempting edits on base images and a couple of questions came up > when re-running through the pipeline: > > 1. After cp, wm, or pial edits on the base image, is it okay to > simply start at ‘-autorecon2’ or must the specific starting points be used? > (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”). > > > 2. When re-running a base, after edits, starting at autorecon2, is it > necessary to include all the timepoints in the command like (ie. “-tp subj1 > –tp subj2”)? It’d make things simpler if that wasn’t necessary and our > reading of the longitudinal processing protocol seems to suggest all the > “tp” related stuff happens in autorecon1 when the norm image and > transformations are generated. After that, the doc suggests that it simply > processes that averaged image per-usual. > > > Thanks in advance for any help! > > *Corrina Fonseca* > Staff Research Associate II > > Senior Imaging Technician > *Center for Imaging of Neurodegenerative Diseases* > > *San Francisco VA Medical Center* > > *4150 Clement Street (114M)* > > *San Francisco, CA 94121* > > *http://www.radiology.ucsf.edu/cind <http://www.radiology.ucsf.edu/cind>* > > *(415) 221-4810 x23088 <(415)%20221-4810>* > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ---------- Forwarded message ---------- > From: peng <prion.w(a)gmail.com> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Thu, 23 Feb 2017 12:58:31 +0100 > Subject: Re: [Freesurfer] FS 6.0 Freeview > Dear Ruopeng, > > I have the same problem even before the current version 6 release, and > it was "solved" by invoke freeview from the command line (term). I guess, > to start from the icon, it might use different setup files. > > best > Peng > > On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > wrote: > > Or would it be possible to send us the full crash report? > > On Feb 17, 2017, at 10:17 AM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > > Hi Dan. Is there an error output to the screen or terminal window? We > will probably need that to help diagnose the issue. > > > > On 02/17/2017 05:31 AM, Daniel Carey wrote: > > Dear All, > > I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable > to load volumes in Freeview. When selecting 'File > Load volume', the > dialog box appears, but when I select any T1.mgz and click Ok, Freeview > immediately crashes. > > Has anyone encountered this same issue? > > Best wishes, > > Dan > > --- > Dr. Daniel Carey > Post-Doctoral Research Fellow - Statistician > The Irish LongituDinal Study on Ageing (TILDA) > Trinity College Dublin > Dublin 2, Ireland. > Email: careyda(a)tcd.ie <mailto:careyda@tcd.ie <careyda(a)tcd.ie>> > > > > _______________________________________________ > 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 > > > > _______________________________________________ > 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. > > > > > > ---------- Forwarded message ---------- > From: Kevin Aquino <aquino.km(a)gmail.com> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Thu, 23 Feb 2017 23:45:10 +1100 > Subject: Re: [Freesurfer] FS 6.0 Freeview > > I've had the same problem, > the only solution I have is to only open Freeview from terminal > > Cheers, > Kevo > > On 23 Feb 2017, at 10:58 pm, peng <prion.w(a)gmail.com> wrote: > > Dear Ruopeng, > > I have the same problem even before the current version 6 release, and > it was "solved" by invoke freeview from the command line (term). I guess, > to start from the icon, it might use different setup files. > > best > Peng > > On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > wrote: > > Or would it be possible to send us the full crash report? > > On Feb 17, 2017, at 10:17 AM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > > Hi Dan. Is there an error output to the screen or terminal window? We > will probably need that to help diagnose the issue. > > > > On 02/17/2017 05:31 AM, Daniel Carey wrote: > > Dear All, > > I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable > to load volumes in Freeview. When selecting 'File > Load volume', the > dialog box appears, but when I select any T1.mgz and click Ok, Freeview > immediately crashes. > > Has anyone encountered this same issue? > > Best wishes, > > Dan > > --- > Dr. Daniel Carey > Post-Doctoral Research Fellow - Statistician > The Irish LongituDinal Study on Ageing (TILDA) > Trinity College Dublin > Dublin 2, Ireland. > Email: careyda(a)tcd.ie <mailto:careyda@tcd.ie <careyda(a)tcd.ie>> > > > > _______________________________________________ > 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 > > > > _______________________________________________ > 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. > > > > > ---------- Forwarded message ---------- > From: Randolph Andrews <randrews(a)admdx.com> > To: <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Thu, 23 Feb 2017 08:33:25 -0600 > Subject: [Freesurfer] Virtualbox for FS v6.0 ? > > In past releases of FreeSurfer, there had been a version of the software > suite contained in a VirtualBox (alongside the MacOS and Linux versions). > Currently, I only see Mac & Linux. Is there a plan to release a VirtualBox > edition of 6.0 ? > > > > ---------- Forwarded message ---------- > From: Trisanna Sprung-Much <trisanna.sprung-much(a)mail.mcgill.ca> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Thu, 23 Feb 2017 11:48:26 -0500 > Subject: [Freesurfer] recon-all error (6.0) > Hi All > > I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it > stops when trying to transform to the "conformed" space. I get the > following error after about a minute. I have not seen this error before. > > mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like > orig.mgz --conform > mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like > orig.mgz --conform > ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF file > miopen: MINC package entry point > Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc > mincRead(): error reading volume from file > ./tmp.mri_nu_correct.mni.2860/nu1.mnc > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc... > Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC > 2016 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > Any ideas? > > Best > > Trisanna > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > > > > ---------- Forwarded message ---------- > From: "Worker, Amanda" <amanda.worker(a)kcl.ac.uk> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Thu, 23 Feb 2017 16:55:09 +0000 > Subject: [Freesurfer] deformation fields > > Hi All, > > > I am trying to use the subcortical segmentation of regions from the > longitudinal template to propogate to each time point using deformation > fields. > > > Does anyone know how if this is possible and if so, how can I do it? > > > Thanks in advance, > > > Amanda > > > > > > ---------- Forwarded message ---------- > From: Jing Gu <gujing2009(a)gmail.com> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: > Bcc: > Date: Thu, 23 Feb 2017 11:55:59 -0500 > Subject: [Freesurfer] How to output particular area from stats subdir > Dear FreeSurfer Developers, > By using the following code, we can get volume data of different areas > from stats file. > asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt > > How can I get information of one or two areas, such as hippocampal? thanks > > Best, > Gina > _______________________________________________ > 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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Ct file
by yusif Al-kheder 27 Feb '17

27 Feb '17

Hello, Is there a way to use freesurfer to get coordinates and volume information from a ct file? Youssif

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Manual edit to include missing cortex?
by Rockers, Elijah D. 27 Feb '17

27 Feb '17

Is there something I can do to extend the pial surface to include cortex that it ignored? In some places there are rather large chunks of cortex not included in the pial surface. http://imgur.com/a/FnAgj Link is to a screenshot, notice the top of the brain. It's fairly pronounced, visible in 12 adjacent sagittal slices. I tried using the "Reposition Surface" tool, but I'm not exactly how it works, and I ended up just making the surface look crazy there. I also tried adding control points in the white matter near the edges of the WM surface by the problem and ran the reconstruction, as someone in the archives suggested, but it didn't change the surface. Thanks for your help, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Intensity information of Hippocampal Subfields
by ali reza mohammadi nejad 27 Feb '17

27 Feb '17

Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command? Thank you in advance for any help. Alireza

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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg
by Antonin Skoch 27 Feb '17

27 Feb '17

Dear Doug, thank you for the feedback. In this context I would like to ask you to share your opinion on the mri_cvs_register. This tool should be far the most accurate for the registration to MNI, than any of affine-based registration tools, shouldn't be? Are there any pitfalls/disadvantages (apart from huge demand on computing resources) of using this tool? Since you mentioned that you usually use mni152reg, could you share the reason why do not use mri_cvs_register as the preferential tool for registration to MNI? Regards, Antonin I have not actually tested it on the mni152 reg. It might (probably does) work fine. On 2/25/17 5:33 PM, Antonin Skoch wrote: Dear Doug, I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to MNI? According to help, mri_coreg is also able to do 12 DOF registration. Antonin mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use normalized mutual info. bbregister uses the BBR cost function and is preferred for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote: Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
by Antonin Skoch 27 Feb '17

27 Feb '17

Dear Paul, I think that the transform window in freeview opens by default to enable manual refinement of registration if needed. If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be tkregister2 --mov your_moveable --targ your_target --reg your_lta or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs Antonin Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? ‎Thanks. Best, Paul Sent from my BlackBerry 10 smartphone. From: Antonin Skoch Sent: Sunday, February 26, 2017 3:50 PM To: freesurfer(a)nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fw: PETsurfer mri_coreg problem Dear Paul, LTA means transformation matrix stored in .lta format. This matrix can encode transformation between various coordinate spaces. What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox. The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered. Btw, does the alignment of the images seem reasonable? How does it look in tkregister2? Regards, Antonin

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