[Freesurfer] Longitudinal analysis with QDEC

Hello Dear FreeSurfer Developers, Thank You once again for helping me a couple of months ago. Today I came across a new obstacle, as I have been trying to analyse longitudinal material. I have performed all preparation steps and I started performing statistical analysis in Qdec when receiving fo

Re: [Freesurfer] Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"

My guess is that you are using Safari on a Mac OSX Machine? If so, I have observed that Safari has strange behavior with ftp links. Can you try using another browser like Firefox or Chrome? Or, you can download by typing the following command in a terminal window: $> curl -O ftp://surfer.nmr.m

Re: [Freesurfer] Longitudinal analysis with QDEC

Hi Pawel, your directory naming looks a little weird. What is the subjects directory ? Are all your subjects (all cross, base and long of all subjects) in CT_10? What is BLD013_ is that the name of the base (=subject template)? Did you run the long_mris_slopes command (follow instructions here

[Freesurfer] nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?

Hi, I'm analyzing data from a collaborator who used SPM to generate some niftis, and freesurfer is unable to read these. I get the following error: nifti1Read(): unsupported slice timing pattern 5 Someone previously had

Re: [Freesurfer] nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?

try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert On 10/23/2015 12:28 PM, Alex Kell wrote: > Hi, > > I'm analyzing data from a collaborator who used SPM to generate some > niftis, and freesurfer is unable to read these. I get the following > error: > nifti

[Freesurfer] Head circumference

Dear FS experts, I want to inquire if there is any script in Freesurfer that can help to calculate the head circumference from MPRAGE ? Thanks for any advice!       Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman

[Freesurfer] Funcroi-Table-Sess Error

Hi there, I ran the following analysis commands: mri_cor2label --c /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi

Re: [Freesurfer] Help with V6

Hello Noah, Could you be more specific as to how you were able to resolve this problem? What additional tweaks were necessary? I too received the same error message: ERROR: Flag -subfields-T1 unrecognized. -all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1 Darwin glenn-stebbins-computer.local 12

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

Hi, I recently using Freesurfer 6 beta version to recon high resolution data with the -cm flag, however, the program exit with error. total defect index = 0 \n mris_euler_number ../surf/rh.orig \n Darwin AlbertStekiiMac 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root: