Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Recon-all w/ Hammersmith atlas
by Ryan Flores 24 Apr '18

24 Apr '18

Hi Freesurfer Developers, Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-…) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward? Thank you for your time. I look forward to hearing from you. 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1) Best, Ryan -- Ryan Flores Clinical Research Coordinator

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resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

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Re: [Freesurfer] Non-rigid registration approaches
by Hedyeh Javaheri 24 Apr '18

24 Apr '18

External Email - Use Caution Thanks for your reply Douglas, I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer? Thanks -Hedyeh ------------------------------------------------------------ ----------------------------------------------------------------- Date: Tue, 17 Apr 2018 11:49:04 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Non-rigid registration approaches To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <763da2ef-359a-9f44-9b54-1f96acb3b2ef(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: > Hello all, > > I am performing DTI analysis and wanted to know if Freesurfer has a > tool for non-rigid registration. > I performed recon-all and dt_recon on my subject and then used the > register.dat file that was generated by dt_recon to convert the > dt_recon output files back into the space of my orig.nii file from the > recon-all output. Now I need to register the files in the orig.nii > space back onto the T1 MRI that is in native space. > > I have tried using? mri_vol2vol to get the files in the orig.nii > (recon-all) space into the T1 native space without using a > registration file (I used --regheader) and now the registration matrix > of my file is the same as the native space, but when I use rview to > visualize the registration there are flaws. I've also tried this > co-registration using tkregister2 to create a registration file called > register.native.dat, and then used mri_vol2vol with > register.native.dat; and the results were the same as when I used > mri_vol2vol with --regheader. > > Is there a tool to do actual manual registration in Freesurfer? Using > tkregister2 I cannot perform localized changes; and the global changes > it is capable of do not improve on the coregistration. > > Here is a breakdown of what I have done: > > subject in Native space to Freesurfer conformed space using recon-all, > output: orig.nii > subject in Native space to other Freesurfer space using dt_recon, > output: lowb.nii and register.dat > From the other Freesufer space to Freesurfer conformed space using > register.dat, output: lowb2orig.nii > attempting to convert from Freesurfer conformed space to Native space: > ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration > ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then > mri_vol2vol and ?register.native.dat --> poor registration > > I am running Freesurfer version 6 on Windows. > > Thanks in advance! > -Hedyeh Javaheri

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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
by Douglas Greve 24 Apr '18

24 Apr '18

please remember to post to the list ... Run tkregister --mov negative_allsocial_proportion.nii --regheader --reg deleteme.lta --s collin --surfs where collin is the name of the subject you gave when you analyzed the collin brain in recon-all. If this looks like it is in register, then using --regheader with mri_vol2surf should work. If it is not, then tkregister --mov negative_allsocial_proportion.nii --identity --reg identity.lta --s collin --surfs If that looks ok, then save the registration and use that when running mri_vol2surf On 4/20/18 3:48 PM, srishti goel wrote: > > External Email - Use Caution > > Hi Douglas, > > Following up on where I left, our maps > (negative_allsocial_proportion.nii) were created using *neuroelf > *software and can be viewed in neuroelf on the *Colins template* > (colin_brain_ICBMnorm.vmr). I exported this template as a nifti file > and did recon-all for this file but I am still stuck with the same > issue. I can run mri_vol2surf on our maps using the colins template > but then how do I compare the maps that I am trying to compare because > the other map in on the surface of MNI template in FS. I want to be > able to produce the two maps on the same surface. > > Please let me know if you have thoughts about it. > > Thanks so much! > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu <mailto:srishtig@email.unc.edu> > skype: srishti.goel12 > > > On Thu, Apr 12, 2018 at 10:51 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > Hi Srishti, you will need to be much more specific to allow me to > help you. mni152_subject is not a file that can be input to > recon-all (it should be a dicom or nifti or mgz). If you use the > same input to recon-all that you used to view it in spm, then the > FS output should align with your map. > > > On 04/12/2018 10:41 AM, srishti goel wrote: > > mni152_subject is the file that has been used for recon-all. > Our collaborators had run recon-all with that file so we did > not do it again. As far as the 'MNI template' is concerned, I > didn't do that part of the analysis so I am unsure which > specific file it is, but it MNI 152. > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > skype: srishti.goel12 > > > On Thu, Apr 12, 2018 at 10:28 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> wrote: > > What is the "MNI template" that you are using. I mean an > exact file > used. Did you use this file when you ran recon-all? > > > On 04/12/2018 10:23 AM, srishti goel wrote: > > Yeah, I am unsure where to go from here as well. So the > results > can be > > viewed in SPM and on the MNI template space itself, > since SPM > > typically does not have a problem showing multiple images in > different > > sizes. > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > skype: srishti.goel12 > > > > > > On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve > > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> > wrote: > > > > When you use bbregister, it is expecting the input > nii file to > > represent > > the actual anatomy of the subject, so it does not > surprise > me that it > > does not work that well. I'm not sure what to do > about this > because a > > meta analysis image will never have decent anatomy. In > theory, it > > should > > be already in alignment with the mni152, but this is > trickier than it > > seems. How do you usually view the results? In FSL > or SPM? > Do you view > > them on an anatomical image? > > > > > > On 04/12/2018 09:03 AM, srishti goel wrote: > > > Hi Douglas, > > > > > > The negative_allsocial_proportion.nii file has > actually been > > converted > > > from a vmp file - 'negative_allsocial.vmp'. We used > neruoelf to > > > convert the vmp file, option - 'export to analze' and > 'export to > > > nifti'. The original vmp file represent the > results of a > > meta-analysis. > > > > > > Let me know if that helps or you would need more > information. > > > > > > Thanks! > > > > > > Best, > > > Srishti > > > > > > Best, > > > Srishti > > > Social/Clinical Research Specialist > > > Child Imaging Research and Life Experiences Lab > > > University of North Carolina at Chapel Hill > > > email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > > > skype: srishti.goel12 > > > > > > > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > > > <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > > > > > how was negative_allsocial_proportion.nii created? > > > > > > > > > On 4/11/18 9:14 PM, srishti goel wrote: > > >> Hi, > > >> > > >> I used bbregister to register: > > >> bbregister --mov > negative_allsocial_proportion.nii --s > > >> mni152_subject --bold --lta register.lta > > >> and then viewed it using: > > >> tkregisterfv --mov > negative_allsocial_proportion.nii > --reg > > >> register.lta --surfs > > >> It doesn't look great but it still looks okay > (Screenshot > > attached). > > >> Then I also used lta in tkregisterfv, as: > > >> tkregisterfv --mov > negative_allsocial_proportion.nii > --reg > > >> register.lta --s mni152_subject --surfs --reg > reg.deleteme.dat > > >> In this file, the volume map still lies > outside the > surface. > > >> Could you please help me resolve this issue. > > >> I tried using register.lta file in the > mri_vol2surf > but the > > >> overlay map doesn't show up again. > > >> Thanks! > > >> > > >> Best, > > >> Srishti > > >> Social/Clinical Research Specialist > > >> Child Imaging Research and Life Experiences Lab > > >> University of North Carolina at Chapel Hill > > >> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >> skype: srishti.goel12 > > >> > > >> > > >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve > > >> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > >> > > >> don't use --init-rr ( you don't need to > spec an > init in > > >> version 6) > > >> > > >> > > >> On 4/10/18 9:48 PM, srishti goel wrote: > > >>> When I run bbregister, it gives me an error. > Attached > > is the > > >>> register.dat.log file for it. > > >>> Error: > > >>> > > >>> reading source > './tmp.bbregister.91068/template.nii'... > > >>> > > >>> mri_robust_register.bin: only pass single frame > MRI source > > >>> ./tmp.bbregister.91068/template.nii. > > >>> > > >>> > > >>> No such file or directory > > >>> > > >>> > > >>> Any help is greatly appreciated! > > >>> > > >>> > > >>> Best, > > >>> Srishti > > >>> Social/Clinical Research Specialist > > >>> Child Imaging Research and Life > Experiences Lab > > >>> University of North Carolina at Chapel Hill > > >>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >>> skype: srishti.goel12 > > >>> > > >>> > > >>> On Tue, Apr 10, 2018 at 11:07 AM, > Douglas Greve > > >>> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> > > wrote: > > >>> > > >>> They are not in registration. Try > running > > bbregister to > > >>> create a registration file (lta), > then pass > the lta to > > >>> tkregisterfv instead of --regheader > > >>> > > >>> > > >>> On 4/9/18 11:49 PM, Bruce Fischl wrote: > > >>>> How did you generate the > registration? And give > > us the > > >>>> details of what you are trying to > register > > >>>> Cheers > > >>>> Bruce > > >>>> > > >>>> On Apr 8, 2018, at 2:55 PM, srishti > goel > > >>>> <23srishtigoel(a)gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>> > > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>>> > > >>>> <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>> > > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>>>>> wrote: > > >>>> > > >>>>> Hi Bruce, > > >>>>> > > >>>>> Thanks so much for pointing that > out, I > totally > > missed > > >>>>> that part. > > >>>>> > > >>>>> Also, the registration definitely > isn't > appropriate. > > >>>>> Could someone please guide me how to > correct this > > >>>>> problem. I have attached a > screenshot of > how it > > looks > > >>>>> like currently. > > >>>>> > > >>>>> > > >>>>> <Screen Shot 2018-04-08 at 2.53.33 > PM.png> > > >>>>> > > >>>>> Best, > > >>>>> Srishti > > >>>>> Social/Clinical Research Specialist > > >>>>> Child Imaging Research and Life > Experiences Lab > > >>>>> University of North Carolina at > Chapel Hill > > >>>>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Sun, Apr 8, 2018 at 11:00 AM, > Bruce Fischl > > >>>>> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>>> wrote: > > >>>>> > > >>>>> Hi Srishti > > >>>>> > > >>>>> the directory you are in doesn't > matter. YOu > > >>>>> either need to set SUBJECTS_DIR in the > > >>>>> environment, or use --sd <SUBJECTS_DIR> to > > specify the > > >>>>> directory that contains your subjects. I > > think you > > >>>>> can also give it the full path > to a target > > volume > > >>>>> if you want, but maybe Doug can > comment as he > > >>>>> knows this stuff better than I do > > >>>>> > > >>>>> cheers > > >>>>> Bruce > > >>>>> > > >>>>> > > >>>>> > > >>>>> On Sun, 8 Apr 2018, srishti > goel wrote: > > >>>>> > > >>>>> When I type this > command:tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> It gives me the error: cannot find > > mni152_subject. > > >>>>> Although I clearly checked that the > > directory > > >>>>> from which I am submitting this > command > > has the > > >>>>> mni152_subject directory within which there > > >>>>> are all the other required > directories such > > >>>>> as: mri, > > >>>>> stats, surf, scripts, etc. > > >>>>> > > >>>>> I am unsure what is happening here. > > >>>>> > > >>>>> > > >>>>> Best, > > >>>>> Srishti > > >>>>> Social/Clinical Research Specialist > > >>>>> Child Imaging Research and Life > > Experiences Lab > > >>>>> University of North Carolina at Chapel Hill > > >>>>> email (W): srishtig(a)email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>>>> > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Thu, Apr 5, 2018 at > 12:49 PM, > Douglas N. > > >>>>> Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>> > > >>>>> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>>> wrote: > > >>>>> Those commands look ok. My suspicion > > >>>>> goes to the use of --regheader. See > > >>>>> whether the registration is ok with > > >>>>> > > >>>>> tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> > > >>>>> On 04/05/2018 08:34 AM, srishti > > goel wrote: > > >>>>> > Hi, > > >>>>> > > > >>>>> > I am trying to compare my volume > > maps > > >>>>> > > > (negative_allsocial_proportion.nii) to > > >>>>> someone else's > > >>>>> > (SN_like_cortical_lh.nii.gz) who > > have > > >>>>> it on a surface > > >>>>> > (mni152_subject). So I used the > > steps > > >>>>> for mri_vol2surf command as > > >>>>> > follows: > > >>>>> > > > >>>>> > Commands: > > >>>>> > mri_vol2surf --src > > >>>>> negative_allsocial_proportion.nii --regheader > > >>>>> > mni152_subject --hemi lh --o > > >>>>> ./neg_allsocial_lh.nii --projfrac 0.5 > > >>>>> > Then to view it: > > >>>>> > tksurfer mni152_subject lh inflated > > >>>>> -overlay ./neg_allsocial_lh.nii > > >>>>> > -overlay SN_like_cortical_lh.nii.gz > > >>>>> -fthresh 0.5 > > >>>>> > > > >>>>> > Everything ran fine and we > > didn't get > > >>>>> any error but then while viewing > > >>>>> > the files we could not see our map > > >>>>> (neg_allsocail_lh.nii) on the > > >>>>> > surface. This file seemed to > > work fine > > >>>>> as it is not an empty file when > > >>>>> > I checked the file size. > > However, when > > >>>>> we view it using tksurfer it > > >>>>> > does not show up as a highlighted > > >>>>> portion on the surface. The > > >>>>> > SN_like_cortical_lh.nii.gz file > > shows > > >>>>> up just fine. > > >>>>> > > > >>>>> > Could someone please help me figure > > >>>>> out what might have gone wrong here. > > >>>>> > > > >>>>> > Thanks so much! > > >>>>> > > > >>>>> > > > >>>>> > > > >>>>> > > > _______________________________________________ > > >>>>> > Freesurfer mailing list > > >>>>> > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>>>> > > >>>>> _______________________________________________ > > >>>>> Freesurfer mailing list > > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>>> > > >>>> > > >>>> _______________________________________________ > > >>>> Freesurfer mailing list > > >>>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > > >>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>>> . 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1 0

QDEC vs. Command Line Stream
by Arsenije Subotic 24 Apr '18

24 Apr '18

External Email - Use Caution Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to be the consensus when it comes to using QDEC as opposed to using the command line stream? I've seen QDEC used plentifully in the literature, but I am also aware that it has less glm capability. Thank you for any input! Arsenije

2 1

Re: [Freesurfer] FSGD design for multi-centre study
by C.P.E. Rollins 24 Apr '18

24 Apr '18

Hi Douglas, Thanks for your response. I just wanted to confirm how the FSGD and contrast files might look for the multicentre study. If I'm to create a separate class for each combination of diagnosis, sex, and center, would there then be 24 classes? (as there are 2 diagnoses (patient vs. control), 2 sex, and 6 centres). For instance: GroupDescriptorFile 1 Group control_Male_centre1 Group control_Female_centre1 Group control_Male_centre2 Group control_Female_centre2 Group control_Male_centre3 Group control_Female_centre3 Group control_Male_centre4 Group control_Female_centre4 Group control_Male_centre5 Group control_Female_centre5 Group control_Male_centre6 Group control_Female_centre6 Group patient_Male_centre1 Group patient_Female_centre1 Group patient_Male_centre2 Group patient_Female_centre2 ... Then, my contrast between patients and controls would look like 1 1 1 1 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 for a doss model, if I'm additionally controlling for age, or 24 zeros (instead of 1) for a dods model? Moreover, should I expect any issues with using such a high number of classes? Thanks again, Colleen

3 6

Template recon-all register correction, help needed
by Ting Li 24 Apr '18

24 Apr '18

Hi Freesurfer Experts, I had generated my own template and want to register my subjects into this template. Before the registration, I had run recon-all on my template Once I opened it in freeview, I get something like this. I definitely need to correct these surfaces. Could you give me some suggestions about the areas I pointed out? I am really get lost about them. Thanks a lot. If there has more information about using own template, please send them to me. I am really appreciate your help. Best wishes, Ting

2 1

mri_convert
by Timothy Hendrickson 24 Apr '18

24 Apr '18

External Email - Use Caution Hello, I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker which is a tool that emulates a docker environment but does not require root user privileges in order to do so. Anyway long story short when I attempt to run the udocker container of freesurfer 5.3.0-HCP with the default backend (PRoot) I receive a mmap error with mri_convert which reads: PROT_EXEC | PROT_WRITE. I am able to work around this error in certain instances, but that is not important here. What is important is that when I run a udocker container with freesurfer 6 mri_convert runs without issue. My two questions are: 1) What differences exist between mri_convert between freesurfer 6 and 5.3.0 - HCP 2) Is there any way that I can download/install the newer version of mri_convert used for freesurfer 6 within 5.3.0 - HCP? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay)

1 0

mris_convert Segmentation fault.
by Xiuyi Wang 24 Apr '18

24 Apr '18

External Email - Use Caution Hi, I am planning to convert an ASCII file to a gifti file using mris_convert. I am using FreeSurfer 5.3 on Linux 9 stretch. The ASCII file includes the vertex id , its MNI305 coordinates and p value. Vertex id is 0-based, from 0 to 20483. I used fsaverage5 as the template and extracted the coordinates of each vertex on that surface using the following commands. SW = SurfStatReadSurf({[template_path 'fsaverage5/surf/lh.white'],[template_path 'fsaverage5/surf/rh.white']}); coordis = SurfStatInd2Coord(vertex_id, SW) Then I typed mris_convert file_SW.asc lh_SW.gii # because I learnt that generally surface files starts with a hemisphere specifier. or mris_convert file_SW.asc SW.gii The error message is ERROR: MRISalloc: nfaces=-36 < 0. I guess one possible reason is the first coordinate of the first index is negative (-36). So I generated a new file, replacing all the negative x coordinates with its absolute value - unthreshold_file_SW_abs.asc and then typed: mris_convert SW_abs.asc SW_abs.gii This time the error message is Segmentation fault. Could you please give me any clue how to solve this problem? I also tried this command and it works well, suggesting I can use mris_convert smoothly. mris_convert -v lh.white lh.white.neighbors.asc # Many thanks in advance, Xiuyi Wang

1 0

correcting deffect
by Z Hessam 24 Apr '18

24 Apr '18

External Email - Use Caution Hello FreeSurfer Team i have problem when run a data set, i re-run it but that error remain (just "convex hull" changed from 6148 to 6147!!) this is the last line in terminal (that process doesn't exceed that after about 10 hours!!!) "CORRECTING DEFECT 0 (vertices=21958, convex hull=6147, v0=0)" but the first time i run this data set, there was more another line in terminal: "XL defect detected ..." now i want to know why this error occurred ? and what should i note in my data to never encounter this error again? (I read some similar mails, but i didn't understand my questions) thanks a lot again for your attention

2 1

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Freesurfer April 2018