[Freesurfer] Hippocampal subfields, stuck?

Dear all experts, I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1". Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imag

[Freesurfer] Research Assistant and Psychologist Positions at Max Planck Institute-CBS, Leipzig, Germany

Applications are welcomed for two positions in the Human Communication group lead by Katharina von Kriegstein at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany. Research in the group focuses on the investigation of neural mechanisms of human communi

[Freesurfer] How to find the information from MRI data file

Hi, How can I find the following information from the MRI volume data already preprocessed with Freesurfer. 1. Echo time 2. Repetition time 3. Flip angle Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

[Freesurfer] white matter edits not incorporated

Hi, I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 none of the edits were incorporated. Is the F

Re: [Freesurfer] How to find the information from MRI data file

use mri_info cheers Bruce On Mon, 18 Apr 2016, Muhammad Naveed Iqbal Qureshi wrote: Hi, How can I find the following information from the MRI volume data already preprocessed with Freesurfer.   1.   Echo time 2.   Repetition time 3.   Flip angle Thank you.   Best Regards,

[Freesurfer] lme model for within-subjects repeated measures design

Dear FreeSurfer experts I have one question regarding my data analysis and would be extremely thankful for any advice! My data-set is as follows: I have repeated measures (time point 0 (T0), time point 1 (T1)) of several subjects. All individuals underwent an intervention at one of the tim

Re: [Freesurfer] How to find the information from MRI data file

Hi Bruce, I just ran it out of curiosity on T1w 3D-MPRAGE images from a Siemens scanner which has been converted to nifti using dcm2nii and I got this: TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees Which doesn't look correct? any comments? Thanks, Mahmoud On Mon, Apr 18, 2016 at 11:3

Re: [Freesurfer] How to find the information from MRI data file

Hi Mahmoud nifti doesn't have slots for these parameters so converting through nifti will lose them. Try running it on one slice in the right dicom series cheers Bruce On Mon, 18 Apr 2016, Mahmoud wrote: Hi Bruce, I just ran it out of curiosity on T1w 3D-MPRAGE images from a Siemens scanne

Re: [Freesurfer] How to find the information from MRI data file

The nifti format is bad, and lacks that data, this will only work on mgz files or dicoms. hth d On Mon, Apr 18, 2016 at 11:54 AM, Mahmoud wrote: > Hi Bruce, > > I just ran it out of curiosity on T1w 3D-MPRAGE images from a Siemens > scanner which has been converted to nifti using dcm2nii and I g

[Freesurfer] CA2 hippocampal subfield in FS6.0

Dear FreeSurfers, I was running the FS 6.0 hippocampal subsegmentation and was wondering where the CA2 subfield disappeared to. Version 5.3 had a CA2-3 label, but in 6.0 I can only find CA3, is it implicated that CA2 is part of CA3 as well in 6.0? Sincerely, Patrick Sezen _

Re: [Freesurfer] temporal lobe pial surface problem

Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macar...@libero.it; j...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

I can open the nii.gz output of the first step (vol2vol) just fine. But the .label output of the second step (cor2label) won't open in tksurfer or freeview. When I try to open it in freeview from the command line (freeview -l ) I get: [0]PETSC ERROR: ---

Re: [Freesurfer] temporal lobe pial surface problem

hi Xiaomin, it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effect

Re: [Freesurfer] temporal lobe pial surface problem

It's tough to make out much from the snapshots, if you upload the entire subject dir to our ftp site I'll take a look Cheers Bruce > On Apr 18, 2016, at 7:13 PM, Xiaomin Yue wrote: > > Hi Jon, > > Thanks for your answers. There is gray-white contrast in the temporal lobe, > but same as you