Re: [Freesurfer] hippocampus subfields with T2

External Email - Use Caution Um this is an empirical question. I would try with and without, and then decide. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexo

[Freesurfer] mri_fill unsuccessful in macaque

External Email - Use Caution Hello, I am trying to generate an inflated surface for a macaque brain, but mri_fill has stopped working for this subject. Below is my command line and output. I specify the corpus callosum and pons as well. Any suggestions? mri_fill -CV 101 100 66

[Freesurfer] hippocampus subfields with T2

External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2-space. Is it possible or even recommended to try and generate better hippocampal segmentation in fressurfer 6.0 using both the T1 and T2,

Re: [Freesurfer] Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer

On 08/30/2018 02:24 PM, M. Jordan wrote: > > External Email - Use Caution > > Hello, > > considering the surface 'lh.pial' of the reconAll process: > > When I apply 'mris_convert' in order to convert to .vtk, there is a > shift with respect to the .pial file when viewing in freeview. >

Re: [Freesurfer] MRIread error

The error message you mention ("... could not open file"). Is not in this recon-all.log file. On 08/30/2018 04:23 PM, Song, Da-Yea wrote: > External Email - Use Caution > > I have attached the recon-all.log file for a different subject with the same > error. Hope this helps! > > Thanks,

[Freesurfer] Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer

External Email - Use Caution Hello, considering the surface 'lh.pial' of the reconAll process: When I apply 'mris_convert' in order to convert to .vtk, there is a shift with respect to the .pial file when viewing in freeview. When using the --cras_correction option for convertin

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

External Email - Use Caution Thanks Martin, Yes, I did mean to have the right hemisphere added to the left hemisphere as a new time point. Can you explain on what you mean by run every subject only once? Do you mean to run xhemi for all of the subjects and then run a paired anal

[Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

External Email - Use Caution Dear colleagues, I was wondering if resampling voxel size is done during recon-all. Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be p

[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Hi; My Linux machine has FreeSurfer 6.0 with MATLAB runtime2012bLinux (MCRv80) which allows me to do the hippocampal subfields segmentation without errors. Now, I'd like to use [segmentHA_T1.sh] for hippocampal and nuclei of the amygdala segmentation w

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

External Email - Use Caution Hello Martin: I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that came with it by default). If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat or .stats file. I only get .mgh file in surf folder. I need

[Freesurfer] Fwd: Biomedical Research Engineer Position

External Email - Use Caution Title : *Biomedical **Research Engineer* No. of Position(s): One (1) position Location : Paris, France Starting date : November 2018 *JOB DESCRIPTION* The successful applicant wil

[Freesurfer] Fwd: Postdoctoral Position on Imaging Genetics

External Email - Use Caution Title : *Postdoctoral Position on Imaging Genetics* No. of Position(s): One (1) position Location : Paris, France Starting date : November 2018 *JOB DESCRIPTION* The successful app

[Freesurfer] Fwd: Biostatistician Position

External Email - Use Caution Title : Biostatistician No. of Position(s): One (1) position Location : Paris, France Starting date : as soon as possible *JOB DESCRIPTION* The successful applicant will work at th

Re: [Freesurfer] freesurfer development version for mac incomplete

The centos dev version can be downloaded from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz. What link can you not access? Best, Andrew From: on behalf of "Scheffler, F, Mev [fre...@sun.ac.za]" Reply-To: FS Help Date: Thursday, August

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

Hi Anwar, what FS version are you using? Also what happens if you omit the --out-pc1 but keep the --do-pc1 ? Also no output with that ending? It should write it to the default location. Best, Martin On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote: > External Email

Re: [Freesurfer] error in longitudinal stream command

Hi Valeria, that is a local install (a frozen version of 5.3 or some modified version from 2013). Can you source the system wide install of 5.3 and test that. source /space/freesurfer/nmr-stable53-env If that fails, try 6.0 source /space/freesurfer/nmr-stable60-env Also make sure all director