[Freesurfer] White matter volumes of different lobes?

Hi all. Is there any fast method to get the total (R+L) white matter volumes of different lobes? I need the: average ratio of temporal lobe wm to total white matter average ratio of parietal lobe wm to total white matter average ratio of frontal lobe wm to total white matter average ratio of occip

[Freesurfer] Recon runs longer than the previous time and exits this time with errors

I was unable to extract parts of the cortex with the commands you had told me to try last time. I realised then that it was because recon hadn't finished running and I was using partially processed data. So I tried running it again. Here below is what I got. Since I'm using a partitioned machine sp

Re: [Freesurfer] volume segmentation corrections

Hi Roser, it's hard to judge accuracy from a single slice. The cc segmentation adjusts for the angle of the head, which can make any single sagittal slice look wrong as the cc is cutting through it at an angle. Try looking at the segmentation in other views. Horizontal can be particularly helfp

Re: [Freesurfer] Recon runs longer than the previous time and exits this time with errors

Hi Janani, do you not have libtiff installed on your system? Maybe your LD_LIBRARY_PATH is incorrect? You should talk to a local sysadmin about it. cheers Bruce On Mon, 22 Mar 2010, Janani Dhinakaran wrote: > I was unable to extract parts of the cortex with the commands you had told > me t

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 56

Hi Janani, I seem to recall that newer distributions (and judging from your kernel it is a rather new distribution) come with libtiff.so.4 instead of libtiff.so.3. My solution to this problem so far just was to symlink libtiff.so.4 to libtiff.so.3. (Just go in the directory where the library li

[Freesurfer] Displaying parcellation labels asegstats2table

I am trying to obtain mean intensities of Destrieux parcellations using the following command. asegstats2table --subjects --meas mean --statsfile lh.aparc.a2009s.stats --tablefile somename.txt But the output text files does not contain any label names. instead it contains the following as o

[Freesurfer] DTI group analysis

Hello all, In trying to perform a group analysis on volumetric and DTI data (with test4d.nii.gz file created by fslmerge), I encounter an error. Any help is greatly appreciated. Also, can anyone tell me what programs they prefer to use for DTI group analysis? It seems QDEC isn't helpful if you n

[Freesurfer] DTI group analysis

Hello all, In trying to perform a group analysis on volumetric and DTI data (with test4d.nii.gz file created by fslmerge), I encounter an error. Any help is greatly appreciated. Also, can anyone tell me what programs they prefer to use for DTI group analysis? It seems QDEC isn't helpful if you ne