[Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

Dear Freesurfers, I tried to generate annotations by using the command mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could not succeed. Any helps would be appreciated. --- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environm

Re: [Freesurfer] Hippocamp subfields

THank you Zeke! Do I have to repeat all the reconall command with the new freesurfer version or I can use the processed files and run only the hippo segmentation? BW Angela > You can download the dev version of freesurfer which contains the new > hippocampal segmentation from the following page:

Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

Is there a file called ./rh.unknown.label ? On 5/25/15 5:37 AM, Liu Y wrote: Dear Freesurfers, I tried to generate annotations by using the command mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could not succeed. Any helps would be appreciated. --

Re: [Freesurfer] hippocampal subfields

Hi FS Experts, I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file Making Unknown map to reduced label 13 Computing hyperparameters for estimation of Gaussian parameters Estimating typical intensities of  alveus /

Re: [Freesurfer] mni305 volume-based analysis

Have you looked at the documentation for FC analysis in FSFAST? It gives sample mkanalysis-sess commands for lh. They are basically the same for rh and mni305 On 5/22/15 7:19 PM, std...@virgilio.it wrote: Hi list, I'm configuring mkanalysis-sess to configure an analysis for FC data by FS-FA

Re: [Freesurfer] Fwd: recon-all issue

The error says: mris_fix_topology: could not read input surface /sc/orga/projects/psychimage/MCIC/Schizophrenia/SiteC/Cooked/A00036129/Freesurfer/A00036129/surf/lh.qsphere.nofix No such file or directory Does that file exist? Have you run out of disc space on that volume? doug On 5/22/15 8

Re: [Freesurfer] Fwd: recon-all issue

Hi Doug, That file does not exist, because none of the surf files got created from this pipeline. So there was an error before that? The mri files got created (partially) and what's there looks good. Missing are: aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.noCCseg.mgz, aseg.auto

[Freesurfer] Getting coordinates in the mni152 template using cvs_mri_register and applyMorph

Hi, I have a list of coordinates from a subject's scan and I want to get the corresponding coordinates in the MNI152 template. I am running the following commands: mri_cvs_register --mov TWH006 --template cvs_avg35_inMNI152 applyMorph --template /mnt/archive/dgroppe/subjects/cvs_avg35_

[Freesurfer] fs-fast primarily voxel based?

Hi all, I am seeking a little clarification regarding fMRI analyses with FS-FAST. In the documentation and supplied PowerPoint presentations there are many references to niftis, and statements like "Performs GLM fit at each voxel". Given this, for the cortex, would I be correct in the assertion t

[Freesurfer] The phase of angle.nii.gz

Dear Freesurfer experts, I saw you answered one email the phase for "polar" is -pi to pi. Could you please expain how the phase represent the location on retina? For example, in my retinotopic experiment, the wedge rotate counterclockwise (start from right horizontal), I wonder how the phase rotat