[Freesurfer] Special image protocol

External Email - Use Caution Dear member, I am really new with this freesurfer, just need to ask 1 question. Is there a special image protocol before running the MRI and then upload it to freesurfer? Please share your thoughts. Thank you for your kind attention and cooperation.

Re: [Freesurfer] mris_preproc error: dimension mismatch

External Email - Use Caution Hi Doug, I'm still trying to troubleshoot my mris_preproc error: dimension mismatch. I don't think qcache was run on the CBF images because they were last processed in SPM (working on old dataset made by someone else)...there aren't any smooth fwhm

[Freesurfer] Fw: clusters annotation file in surface - ERROR

Thank you Doug, As you suggested, I tried to use that command (mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s MS072_R01_04 --hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot) but I got this error on tksurfer: Successfully parsed tksurfer.tcl reading white matter vertex lo

Re: [Freesurfer] mri_convert

External Email - Use Caution mri_convert can do lots of things but I would actually try mri_probedicom to get the DICOM timings. If you have AFNI installed you could also try dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi. You could just loop over dicoms

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution I'll try to find some visual way to show what I mean, but it's really something mild and probably negligible. Do you know if is it possible with mri_vol2vol to give to all the runs that belong to the same subject the same system coordinates? So that eac

Re: [Freesurfer] Fwd: segmentation error

External Email - Use Caution Hi there, Sorry for taking so long to respond but I am a newbie using Linux. I uploaded the files using Martinos Center Filedrop under the subject -- Segmentation error - Mara - old suject file. Thanks, Mara Bruce Fischl escreveu no dia quarta, 20/0

[Freesurfer] mri_convert

External Email - Use Caution hi FS experts. I would like to inquire about the command mri_ convert I use this command to convert fMRI and PET 4D volumes from dicom format to nifti. Are there any flags that can be used in mri_convert command line to enable it to extract a text fi

Re: [Freesurfer] dtrecon

It cannot. It just does simple tensor analysis. Not sure what else to use. On 2/20/19 9:02 AM, john Anderson wrote: External Email - Use Caution Hi FS experts, I would like to inquire about the command "dtrecon" in Freesurfer. Is this command able to process multishell diffusion data? if

Re: [Freesurfer] Problem with freeview in linux subsystem for

External Email - Use Caution Hi Falk, Thank you for the reply. Yes, I am running Xming and have set this option in the .bashrc file. I still get the same error. I have tried to research this issue extensively but cannot seem to find the answer. Thanks, Brady ___

Re: [Freesurfer] Fwd: segmentation error

hmmm, I don't see anything glairing in the log. I guess upload the subject and we'll take a look Bruce On Wed, 20 Feb 2019, mara alves wrote: External Email - Use Caution Here is the recon-all.log for one for old subjects.Thanks, Mara mara alves escreveu no dia quarta, 2

Re: [Freesurfer] Fwd: segmentation error

Hi Mara I mean. cd $SUBJECTS_DIR tar czvf subject.tgz $subject then ftp the resulting subject.tgz file to our ftp site cheers Bruce On Wed, 20 Feb 2019, mara alves wrote: External Email - Use Caution Hi, Thanks for the quick reply. What do you mean about uploading the enti

Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

External Email - Use Caution Hi Doug, I tried what you suggested, but it did not work (see below for details of what we tried). We have TkReg RAS coordinates (or vertex points) for our electrode contacts; most contacts are *deep within the brain* (e.g., hippocampus and amygdala).

[Freesurfer] mri_cc not giving thicker corpus callosum

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the “mri_cc” command to obtain a segmentation of the corpus callosum (CC) that is thicker then the usual 5mm (i.e. 5 voxel in my image). I would like indeed to cover the "entire" CC volume and label it with

[Freesurfer] dtrecon

External Email - Use Caution Hi FS experts, I would like to inquire about the command "dtrecon" in Freesurfer. Is this command able to process multishell diffusion data? if not would you recommend any method? Thanks in advance John___ F

Re: [Freesurfer] Problem with freeview in linux subsystem for windows

External Email - Use Caution Hi Brady, do you run a X server on windows? I run Xming and included in the .bashrc "export DISPLAY=localhost:0.0". Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Williamson, Brady Gesendet: Dienstag, 19. Februar 2019 21:51

Re: [Freesurfer] Fwd: segmentation error

External Email - Use Caution Hi, Thanks for the quick reply. What do you mean about uploading the entire subject? All the output files of the recon -all? Best, Mara Bruce Fischl escreveu no dia terça, 19/02/2019 à(s) 23:10: > wow, that looks pretty bad. Can you send us the rec