Re: [Freesurfer] MP-RAGE protocol

External Email - Use Caution Hi Douglas, I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance. Yours faithfully, Mustafa Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. menulis: H

[Freesurfer] mri_convert issues

External Email - Use Caution Hello, I was trying to convert nifti1 files (.hdr and .img) to nii files using the command: > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz But this error pop-up: mri_convert.bin: unknown flag '-i input.hdr' The same command was wo

[Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities d

[Freesurfer] Partial volume effects - brainstem

External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (grou

Re: [Freesurfer] mri_convert issues

External Email - Use Caution Dear Jennifer, could it be that you are confusing `mri_convert` and `mris_convert` (note the 's')? Best, Tim > On May 16, 2019 at 10:58 AM jennifer sorinas wrote: > I was trying to convert nifti1 files (.hdr and .img) to nii files using the > com

Re: [Freesurfer] recon-all exited ERRORS

External Email - Use Caution Dear Qiannan, I’m having the same problems, recon-all -all command is not working. FreeSurfer Developers help please! 😊 Best, Jennifer Enviado desde Correo para Windows 10 _

Re: [Freesurfer] mri_convert issues

External Email - Use Caution Dear Tim, Thanks for your response. I'm sure that the command is mri-convert (I was using it few months ago without problems). Btw, we are experiencing problems also with the recon-all command at different computers. I don't know which is the error,

Re: [Freesurfer] mri_convert issues

Hi Jennifer try mri_convert -it nifti1 input.img output.nii.gz you might not need the "-it nifti1" are you sure it's a nifti and not analyze? You need to be careful you have the correct direction cosines to make sure you know which is left and which is right. Definitely bring it up in free

Re: [Freesurfer] recon-all exited ERRORS

can you give us more details (command line, screen output, recon-all.log file)? On Thu, 16 May 2019, jennifer sorinas wrote: External Email - Use Caution Dear Qiannan, I’m having the same problems, recon-all -all command is not working. FreeSurfer Developers help please! ?

Re: [Freesurfer] MP-RAGE protocol

Hi Mustafa can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log? cheers Bruce On Thu, 16 May 2019, mustafa amin wrote: External Email - Use Caution Hi Douglas, I tried to follow the instruction to recon-al

Re: [Freesurfer] mri_convert issues

External Email - Use Caution Dear Jennifer, if your nifti1 files are named 'brain_nii.hdr' and 'brain_nii.img', try the following: mri_convert brain_nii --out_type nii brain2.nii Best, Tim > On May 16, 2019 at 12:38 PM jennifer sorinas wrote: > > > External Em

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution ​Hello Caspar, So far, I have not found a CentOS rpm with that 2.14 version of libcrypt, but you can download the source from the GNU project and try building it on your machine with the following steps. - R. 1) Become root in your terminal window an

[Freesurfer] brainstem - partial volume effects

External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (grou

Re: [Freesurfer] brainstem - partial volume effects

External Email - Use Caution Hi Dusan, Volumes are computed from soft segmentations, which ameliorates the problems with partial voluming with the surrounding CSF. Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://

[Freesurfer] brainstem - partial volume effect

External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (grou

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

Can you send the command line and full terminal output? On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > We are getting segmentation fault (core dumped) error when trying to > run mri_convert on NIFTI files. This is running Freesurfer v5.3 on >

[Freesurfer] Generating cortical correspondence vectors

External Email - Use Caution Hello FreeSurfer Developers, I'm interested in regenerating cortical correspondence vectors between pial and white surfaces as described in "Microstructural parcellation of the human brain." Is this currently the default way that freesurfer extracts

Re: [Freesurfer] MP-RAGE protocol

External Email - Use Caution Hi Bruce, Herewith I attach within the email the command that didn't work when I wanted to reconall. Please have a look. What about the previous dicom that I have sent to you? Please share some thoughts.Thank you very much. Yours faithfully, Mustaf