[Freesurfer] question about "mean curvatura"

Dear FreeSurfer Group, Sorry for interrupting. I am Hui Li, a researcher fron Beijing, China, interesting in sMRI of mind disorder. Recently, I am working on some data about schizophrenia. I compared the patients and healthy controls, and found that the main difference between these two grou

[Freesurfer] [FSL or FREESURFER] SIEMENS FIELDMAP B0 UNWARPING FOR DTI

Hello FSL and FS pros, I am trying to pre process DW images but am not sure how to unwarp images. We are using Siemens Skyra 3T and output fieldmaps; 2 files output from the scanner; the first file contains two magnitude files in one the second file contains the single phase difference image --

[Freesurfer] PETsurfer surface based analysis

Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness? b) What is the difference between mris_preproc and mri_conca

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad, There is a “secret” way of getting the posteriors. You need to set the environment variable WRITE_POSTERIORS to 1 before you call recon-all. In (t)csh: setenv WRITE_POSTERIORS 1 In bash: export WRITE_POSTERIORS=1 And then call recon-all -hippocampal-subfields-T1(T2) as usual. The discr

[Freesurfer] Hippocampal Subfields Posterior Probability

Hello Dr. Iglesias, I'm currently examining the distributions of the posterior probabilities of the different hippocampal subfields, and I'm interested in obtaining the probability distribution images for the subfields that correspond to the volumes output in the subjects text file. While I

[Freesurfer] [FSL] Re Orient image from AP to PA axis

Dear all, I would like to if there is any procedure to reorient the image ( flip ) from AP axis to PA , I have around 50 scans all of which are scanned in A/P axis and i would like to reorient them , kindly please let me know if there is any procedure. I tried mri_convert and orient_mri is freesu

Re: [Freesurfer] Custom brain segmentation to equal sized regions

Hi David mris_make_face_parcellation can do what you want for the cortex. If you use the sphere used for cross-hemisphere registration as input I think (Hopefully Doug can tell us what it is called) cheers Bruce On Tue, 21 Mar 2017, david.kam...@pet.wayne.edu wrote: > Freesurfers, > > Is

[Freesurfer] Custom brain segmentation to equal sized regions

Freesurfers, Is there a way to segment each hemisphere to an identical number of equal sized regions which are as close in size and location as possible to their contralateral homotopic regions. Eg. I’d like to segment the left hemisphere to regions with a 2 cm2 surface and do the same for the rig

Re: [Freesurfer] display SPM results on inflated surface?

Hi Doug and others, A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is th

Re: [Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

Hi Veronica it's because you are mixing versions. Can you rerun your subject with 6.0 from scratch? cheers Bruce On Tue, 21 Mar 2017, Veronica Munoz wrote: Dear all, I'm trying to add FLAIR data to a subject. I did the first ("classic") recon-all on a platform so I get the following warning

[Freesurfer] white matter volumes for frontal and temporal lobes

Hello I need separate grey and white volumes for the frontal and temporal lobes. I have values for grey volume from the following... mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation mris_anatomical_statson the lh.lobar_annotation.annot file to generate a text file.

[Freesurfer] White matter volume in each lobe

Hello I need separate grey and white volumes for the frontal and temporal lobes. I have values for grey volume from mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation mris_anatomical_statson the lh.lobar_annotation.annot file to generate a text file. I've also run

[Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

Dear all, I'm trying to add FLAIR data to a subject. I did the first ("classic") recon-all on a platform so I get the following warnings: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-s

Re: [Freesurfer] xhemi label

Hi Doug, I'm not sure how to use this binary. Do I need to install it? Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve wrote: > Are you using v5.3? You will need a version 6. You can get this binary > for v6 here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > >