[Freesurfer] qcache for qdec longitudinal analysis

Hi Freesurfer team, I am planning on following this page for my longitudinal group analysis using QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. However, it tells me to run -qcache for all of my subjects. Since I already ran the -long stream for all my subjects,

Re: [Freesurfer] Support for surface data on NeuroVault.org

Thank you for your comments. Some more questions below: On Mon, Aug 22, 2016 at 1:09 PM, Douglas N Greve wrote: > > > 1. In NeuroVault users are asked to upload their statistical maps in > > form of files. I'm planning to target outputs of mri_glmfit: > > preferably

Re: [Freesurfer] Recon-all error using Freesurfer 6.0

Nothing looks suspicious. Try setting setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir ie, removing the trailing "/" On 08/22/2016 02:12 AM, Elpiniki Andrew wrote: > Hello Freesurfer experts, > > I'm having a bit of difficulty running the recon-all command. I > recently

Re: [Freesurfer] Support for surface data on NeuroVault.org

On 08/20/2016 01:21 PM, Chris Filo Gorgolewski wrote: > Dear FreeSurfer community, > I am one of the developers of NeuroVault.org - > an open repository for vizualizing, analyzing, and sharing of > statistical and parcellation maps of the human brain. So far >

Re: [Freesurfer] Recon-all Correcting Defect 0

It looks like there is a very large defect. Check the wm.mgz file to see if the cerebellum has been removed. On 08/21/2016 08:46 AM, Heidi Foo wrote: > Dear FreeSurfer team, > > I apologize for sending this email again. I am currently running > recon-all for my subjects but for 2 of them, it

Re: [Freesurfer] $SUBJECTS_DIR

There is already a label called ?h.cortex.label for all of cortex. For lobes, you can use mris_annotation2label to break up the annotation into its constituent labels, then use mri_mergelabels to combine subsets into a lobe, then use mris_label2annot to combine the lobes into a new annotation.

Re: [Freesurfer] Structural group analysis

Not sure what you are trying to do. Are you comparing the average thickness in premotor to that in primary motor? What would it mean to visualize that? On 08/22/2016 09:52 AM, Silas wrote: > > Dear FreeSurfer team, > > > I'm doing a structural analysis with around 20 subjects and I'm >

[Freesurfer] Structural group analysis

Dear FreeSurfer team, I'm doing a structural analysis with around 20 subjects and I'm specifically interested in the areas premotor cortex and primary motor cortex. By matlab analysis I've found a very strong statistical significant difference in the cortical thickness when comparing these

[Freesurfer] Recon-all error using Freesurfer 6.0

Hello Freesurfer experts, I'm having a bit of difficulty running the recon-all command. I recently downloaded Freesurfer version 6.0. The command that I'm running is: recon-all -all -s $name -hippocampal-subfields-T1 However I keep receiving this error: If: Expression Syntax I've attached