[Freesurfer] average subject

Hi, I have used make_average_subject and made a new average subject form my N subjects, now I want to load one overlay form a single subject on this new average subject, how should I do that? Regards, Fariba __ Fariba Sharifian, PhD Student. Vi

[Freesurfer] spgr orientation and re-slicing

Dear Experts, I am sorry for the basic question but we have a dataset of subjects we  like to analyze for which  we have different slice thicknesses and orientations in dicom format. All T1's  collected were SPGR volumes with the same scanner parameters. My question was: Do you advice to re-ori

Re: [Freesurfer] spgr orientation and re-slicing

Hi Catherine, no, don't do anything to your data, just run it as it is through recon-all. Also, it is not so good to have different acquisitions in your study (though it does depend a bit on how different they actually all). You should make sure that your study is balanced across the different

Re: [Freesurfer] spgr orientation and re-slicing

Hi Catherine, it shouldn't be necessary, but you should be very careful that any effects you find are biological ones and don't simply reflect acquisition differences. cheers Bruce On Wed, 14 Dec 2011, Cat Chong wrote: Dear Experts, I am sorry for the basic question but we have a dataset o

[Freesurfer] fmcsm5-all.text ::created when?

Hello, Just a quick question.. when is the file (within the bold subdirectories) fmcsm5(4)-all.txt made? Is it created as a result of running func2roi? Thank you! Sandra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h

[Freesurfer] Estimate Brain Volume Fraction

Hi Freesurfer experts, I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct? I am now using freesurfer version 5.0.0 and BrainVolNotVent is not lo

Re: [Freesurfer] average subject

Hi Fariba, use mri_surf2surf to map individual data to another subject (individual or average). doug Fariba Sharifian wrote: > Hi, > I have used make_average_subject and made a new average subject form my N > subjects, now I want to load one overlay form a single subject on this new > average su

Re: [Freesurfer] convert surface label on to functional image

That is the "fill threshold". It indicates how many label points must fall into a voxel in order for that voxel to be considered part of the label. By default it is just over 0, meaning that even one label point falling into the voxel will make that voxel labeled. I would leave it like, look a

Re: [Freesurfer] fmcsm5-all.text ::created when?

Hi Sandra, I'm not sure I know what file you are talking about. What is its exact name? doug swood...@nmr.mgh.harvard.edu wrote: > Hello, > > Just a quick question.. when is the file (within the bold subdirectories) > fmcsm5(4)-all.txt made? Is it created as a result of running func2roi? > > Tha

Re: [Freesurfer] multiple overlay - tksurfer

Have you tried to change the threshold to see if you see more colors? Don't load it as a segmentation, just look at the overlay. doug vin . wrote: > Thank you so much Doug, > > you are right, it doesn't match exactly, however there is some match. > so, now I am running recon-all T1_1mmMNI.nii, p

Re: [Freesurfer] fmcsm5-all.text ::created when?

Hi Doug, the file fmcsm4-all.txt, .../bold/tap_lh_long_CD_R01BTX_pat6_sess1_sm4/caud_LH_t3_5_sm4_75thresh. I think tool using the command 'func2roi-sess' produces this file, but I would like to confirm. An example command we use is: func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_

Re: [Freesurfer] Estimate Brain Volume Fraction

Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with: cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensi

[Freesurfer] Post-Doctoral Position in Neuroimaging at UCSD

Post-Doctoral Position in Neuroimaging on the role of Reward and Inhibition on Appetite Regulation and Behavior A full-time Post-Doctoral position is available to work with Drs. Walter Kaye, Amanda Bischoff-Grethe, and Martin Paulus, Department of Psychiatry, University of California, San Diego

[Freesurfer] ICV and regional brain volumes

We are having a difficult time getting the ICV to fit correctly in our sample, but the segmentions and parcellations look accurate. I believe that the ICV is generated from the talairach.xfm early on in the processing stream, but then further processing for segmentations/parcellations is done.

Re: [Freesurfer] Estimate Brain Volume Fraction

Hi Doug, Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version. Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(to