Re: [Freesurfer] Recon-all error: could not set locale

External Email - Use Caution Hi Bruce, Thank you for your prompt response. Attached is the whole recon-all.log from a failed run. The complete screen output: kt@kt-B85M-DS3H-A:~/Downloads/Thalamus$ ./reconall Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20180703-82d87f8 C

Re: [Freesurfer] Recon-all error: could not set locale

Hi Kayeong can you send us the whole recon-all.log from a failed run and the complete screen output? The locale is needed to specify the format of numbers I believe (e.g. 1,00 vs. 1.00) cheers Bruce On Wed, 4 Jul 2018, ?? ? wrote: External Email - Use Caution Hi Freesur

[Freesurfer] Recon-all error: could not set locale

External Email - Use Caution Hi Freesurfer Team, I am aware that segmentation of thalamic nuclei is only available in developmental versions of Freesurfer. After I have downloaded the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev), I get the following error whene

Re: [Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

Hi Kaley, if you scroll down the log file you should find something like new invocation of recon-all with the correct time stamp and v6 text. The old log is kept and the new one is appended. I am also not sure it is OK to re-run the base with 6.0. It could be that this looks OK in single case

Re: [Freesurfer] Longitudinal processing: cannot find input volume error

Hi Arsenije, I have never seen this. You could try: - convert the norm.mgz to norm.nii.gz and back (keep a backup of the old one) and see if that changes anything - you can also re-run this case from scratch to see if maybe anything else is wrong . Could have been an IO issue. Best, Martin

Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions

Hi Kody, scanner effects across vendor could be larger than disease effects. You can attempt an analysis but you will have a tough time to publish it given these differences and no real way to control for scanner effects. Maybe scan 5-10 people on all these scanners and show that scanner effec

Re: [Freesurfer] Longitudinal errors, Voxel size differs

External Email - Use Caution Thank you so much Martin. This is super and very much appreciated. I'll try this and resample all my data and then hopefully it will run successfully through the longitudinal pipeline over my three time points. Best regards and again thank you for

Re: [Freesurfer] Longitudinal Process

Hi Samir, you can first conform all inputs to 1mm isotropic using mri_convert --conform input output It may make sense to add a covariate in the statistics for the different acquisition to control for a linear effect. Best, Martin > On 25. May 2018, at 08:29, Samir Rekic wrote: > > > >

Re: [Freesurfer] Longitudinal errors, Voxel size differs

Hi Erik, better late then never: you should use mri_convert --conform input output Best, Martin > On 16. May 2018, at 12:19, Erik O'Hanlon wrote: > > External Email - Use Caution > Thank Martin, > > I've been looking into this and it appears that the slight changes in th

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

Hi Tudor, 5.3 had some difficulties reporting image geometry differences even when they were tiny. That was fixed in 6.0. However Bruce’s recommendation (to reslice the second time point exactly as the first) should do the trick. Alternatively (in order to avoid processing bias) you could also

Re: [Freesurfer] recon-all -s 1 exited with ERRORS

Hi Bernardo can you send us the recon-all.log file? cheers Bruce On Wed, 4 Jul 2018, Bernardo Regal wrote: External Email - Use Caution [3f59805705f4d8ccafe6527c8dff34e531a203d9.png?u=2457469] Hi,  Now appears this message: freesurfer-Linux-centos6_x86_64-stable-

Re: [Freesurfer] Geometries-related error from base step & absent norm.mgz

External Email - Use Caution Quick follow-up note in case it will be helpful to anyone experiencing the same problem: I got hold of a Linux machine and installed FreeSurfer 6.0 on it; running these same commands there successfuly produced the norm.mgz file. Therefore, this appears

Re: [Freesurfer] recon-all -s 1 exited with ERRORS

External Email - Use Caution make sure u have 8gb if ram at least Get Outlook for Android From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bernardo Regal Sent: Wednesday, July 4, 2018 12:56:14 PM To: Freesurfer

Re: [Freesurfer] recon-all -s 1 exited with ERRORS

External Email - Use Caution Hi, Now appears this message: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer-v5 FSFAST_HOME /opt/freesurfer-v5/fsfast FSF_OUTPUT_FORMA