[Freesurfer] FOV error

Hi all , I have got a problem with the field of view which is told to be 300 (instead of 240 ou 256) and when running tkmedit it's impossible to have good views ... Can someone tell me the error I did ? Because with other data everything is working . thanks

[Freesurfer] Announcement of HBM satellite conference on the DMN and other Intrinsic Networks

Dear FreeSurfer list, Just to let you know that soon it will be a conference on the Default Mode and other intrinsic networks in Barcelona. It is a satellite of the HBM conference. Please, take a look at the program (see links below) since many interesting people are comming to present their lates

Re: [Freesurfer] FOV error

Hi Antoine, was this acquisition different than the others? 300mm is a pretty big FOV. Are you sure that's correct? If so, then you need to crop it to be 256^3 Bruce On Tue, 27 Apr 2010, Antoine Leflon wrote: > Hi all , > > I have got a problem with the field of view which is told to be 300 >

Re: [Freesurfer] FOV error

Hi , I don't know if it was different , these data were done by someone else . I tried to fit it with the -cw256 flag but it didn't work . Is it possible that data were corrupted or done in a bad way so ? Antoine --- Bruce

Re: [Freesurfer] FOV error

what do you mean by "it didn't work"? On Tue, 27 Apr 2010, Antoine Leflon wrote: Hi , I don't know if it was different , these data were done by someone else . I tried to fit it with the -cw256 flag but it didn't work . Is it possible that data were corrupted or done in a bad way so ? Antoin

Re: [Freesurfer] FOV error

It screened me an error message in the end . It didn't fit the FOV to 256^3 --- Bruce Fischl a écrit : > what do you mean by "it didn't work"? > On Tue, 27 Apr 2010, Antoine Leflon wrote: > >> Hi , >> >> I don't know if it wa

Re: [Freesurfer] question about clustering simulation

Yea, that was a bug in the simulation program I used. I did confirm that the simulations were done on the correct hemisphere. Feel free to edit the files. I'll fix the master when I get a chance. doug James Porter wrote: > Doug- > > Let me be the first to say thank you for saving me massive amo

Re: [Freesurfer] nu-correct parameters

for 3T scans, try this modification to the nu_correct usage in recon-all. first, create a file called 'xopts' with this one line: mri_nu_correct.mni --proto-iters 1000 --distance 50 then, run recon-all with these params: recon-all -s subjid \ -nuintensitycor \ -nuiterations 1 \ -expert /

[Freesurfer] missing stats files

Hi All, In some of our subjects in stats folder i don't see lh and rh .curv.stats files (so only 6 stats files in total whereas in others i have 8 stats files in total) why is that. Recon-all finishes without any error what am i doing wrong. Thanks venkat ===

[Freesurfer] Problem adding control points

Dear FreeSurfers, I'm a postgraduate student and recently started with FreeSurfer. I have problems adding control points to the volumes I have loaded into tkmedit. For some reason, after selecting the Edit Control Points -tool and clicking the white matter voxels, I do not get the green crosses

Re: [Freesurfer] Problem adding control points

Sasa, Are you middle clicking to add a control point? Allison -- On Tue, 27 Apr 2010, Sasa Kivisaari wrote: > Dear FreeSurfers, > > I'm a postgraduate student and recently started with FreeSurfer. I have > problems adding control points to the volumes I have loaded into tkmedit. For > some re

[Freesurfer] recon-all error autorecon3

hi , I was processing autorecon3 and it screened me this error : #...@# Cortical ribbon mask Tue Apr 27 19:44:20 IST 2010 /home/cami/freesurfer/subjects/ant/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_dista

Re: [Freesurfer] recon-all error autorecon3

There are a few suggestions for this from a previous question on the same matter. Please see here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07155.html Allison -- On Tue, 27 Apr 2010, Antoine Leflon wrote: > hi , > > I was processing autorecon3 and it screened me this erro

Re: [Freesurfer] recon-all error autorecon3

Thanks , I'm checking it . Antoine Allison Stevens a écrit : > There are a few suggestions for this from a previous question on the > same matter. Please see here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harv

Re: [Freesurfer] fail to open .mgz data in tkmedit: DICOM image data in the sagittal view

Hi LJ, don't include the "mri" on the command line (it is assumed to be under mri) cheers Bruce On Tue, 27 Apr 2010, liyari5018 wrote: hi FS experts, FS can't recognize the file which was covert from a DICOM data in sagital view, here is an example of failure£º £¨see the annex for mo

Re: [Freesurfer] Saving time in longitudinal processing

Thank you Allison. Does anyone have info about the longitudinal aspect of this question? Imagine this general approach: 1) run autorecon1 on all time points (skip autorecon2-3 since only norm.mgz is needed at this stage) 2) create base template, running autorecon1 and autorecon2 (skip autor

Re: [Freesurfer] fail to open .mgz data in tkmedit: DICOM image data in the sagittal view

Right, your command to see that file should be: tkmedit bai_hong_jun orig/001.mgz Also, it only did the first step because your command was: recon-all -i input -s subjid To run the entire processing stream, you'll want to do: recon-all -all -i input -s subjid Allison -- On Tue, 27 Apr 2010, B

Re: [Freesurfer] Saving time in longitudinal processing

yes, this approach will work if you are only interested in subcortical structures. but an improvement is to use -autorecon2-volonly instead of -autorecon2. the former stops prior to the surface stage. n. On Tue, 2010-04-27 at 15:56 -0400, Jordan Poppenk wrote: > Thank you Allison. Does anyone h

Re: [Freesurfer] Saving time in longitudinal processing

Hi Jordan, this won't work. It is true, that you need only the norm.mgz for the base run, but you need the aseg.mgz and all corresponding transforms of each time point for the longitudinal runs. There might still be a possibility to save time, by only doing the subcortical processing in each ti

Re: [Freesurfer] Saving time in longitudinal processing

Hi Nick and Martin, In that case, in a few subjects, I'll compare the outcome of this limited approach to the results of the full processing stream prior to proceeding. Thank you for your help and suggestions! Cheers, Jordan On 27-Apr-10, at 4:17 PM, Martin Reuter wrote: > Hi Jordan, > > t

Re: [Freesurfer] question about clustering simulation

Hi Doug, This looks very helpful! Should we use the fwhm size corresponding to the argument of the --fwhm flag when recon-all runs mri_surf2surf (for anatomical stats), or round the measure found in the fwhm.dat of the glmfit dir? Thanks, Mike -- Forwarded message -- From: Dougl

Re: [Freesurfer] question about clustering simulation

use the value in the fwhm.dat. I would always round up to be safe. doug Michael Waskom wrote: > Hi Doug, > > This looks very helpful! Should we use the fwhm size corresponding to > the argument of the --fwhm flag when recon-all runs mri_surf2surf (for > anatomical stats), or round the measure