[Freesurfer] data qcached in different FS versions

*Dear Freesurfers,* I have quite a large dataset processed with FS 5.1. However, half of the output was qcached in FS 5.3. I just wanted to clarify whether I should rerun qcache in FS 5.1 for the whole set. If not, could you please confirm that this command does the same across different versions

[Freesurfer] Applying mask with mri_mask

Hi, I would like to apply white matter mask (wm.mgz) produced by freesurfer recon-all command on FLAIR. The FLAIR and wm.mgz have different dimensions such that Flair is 512by512 while wm.mgz has 256by256 in dimensions. I tried to fix this by resizing the flair in matlab but after applying the mas

[Freesurfer] Applying mask with mdi_mask

Hi, I would like to apply white matter mask (wm.mgz) produced by freesurfer recon-all command on FLAIR. The FLAIR and wm.mgz have different dimensions such that Flair is 512by512 while wm.mgz has 256by256 in dimensions. I tried to fix this by resizing the flair in matlab but after applying the mas

Re: [Freesurfer] Saving bbregister result as a volume

Yes, use mri_vol2vol, something like mri_vol2vol --reg register.dat --mov flair.mgh --fstarg --o flair.anat.nii.gz On 01/15/2014 05:10 PM, Arash Jalalian wrote: > Hi free surfer community, > > I am trying to register Flair with T1 using bbregister and save the > result as a volume so I can

Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

Hi Elijah, On 01/15/2014 04:10 PM, Elijah Mak wrote: Hi Martin, Thank you for your help. By re-processing, do you mean running recon-alls all over again? Yes. 5.0 is old and it is better to run everything with 5.3 from beginning to end. If you have a lot of data or a lot of edits, you can

[Freesurfer] Saving bbregister result as a volume

Hi free surfer community, I am trying to register Flair with T1 using bbregister and save the result as a volume so I can open it in my application that I am developing. I managed to obtain the register.dat and also to see the result using tkregister2. I was wondering if I can apply the transform

Re: [Freesurfer] mri_vol2surf - best way to avoid partial voluming?

I always use the 1st option. I've played around with it a bit and have not found that it makes that much of a difference for fMRI data with 3x3x5 voxel size. The default is projfrac=0 for historical reasons. It is just the way that I programmed it when I first wrote it (years ago now), and I'm

Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

Hi Martin, Thank you for your help. By re-processing, do you mean running recon-alls all over again? Could you elaborate on the advantage of creating a new subjectsdir and copying over the orig dirs for each subject? On a related note, would it be better to run the full recon-all pipeline for e

Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

Hi Elijah, if you have minimal edits, I'd recommend to reprocess the data from scratch with 5.3 (that is supposed to be the same as using the -clean flag when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to create a new subjectsdir, copy over the subjedid/mri/orig dirs for eac

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

Hi Janosch, there is no fixed naming convention for subjectids from our side, only recommendations. If you like you can call the first time point of subject1 'mike' and the second time point of the same subject 'peter' , we don't care, but it would be confusing. We recommend a convention whe

Re: [Freesurfer] (no subject)

that usually means that you don't have write permission to pwd cheers Bruce On Wed, 15 Jan 2014, Hugh Pemberton wrote: hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault

[Freesurfer] (no subject)

hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable.

[Freesurfer] mri_vol2surf - best way to avoid partial voluming?

I'd like to project functional data onto the surface for group analysis. I'd like to limit partial voluming when selecting values with mri_vol2surf. I noticed that the default projfrac = 0 for mri_vol2surf which seems to me it would select a number of values contaminated by WM. Why is the default

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

I'll leave this for Martin Bruce On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote: Hi Bruce, thank you very much for your answer! Am 15.01.2014 um 14:33 schrieb Bruce Fischl : Hi Janosch it will certainly make your life easier if you don't change the names. So the subject names are save

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

Hi Bruce, thank you very much for your answer! Am 15.01.2014 um 14:33 schrieb Bruce Fischl : > Hi Janosch > > it will certainly make your life easier if you don't change the names. So the subject names are saved in other places/files than the folder name? > Symlinking is fine if you keep the

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

Hi Janosch it will certainly make your life easier if you don't change the names. Symlinking is fine if you keep the same name, but particularly for the longitudinal runs the names have meaning and are stored in files like the tps one which stores the timepoints that went into the base. chee

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

Hi, sorry if my question was to basic, but I would really appreciate if somebody could give me some insight into whether the folder organization and the subject name used in the first run of recon-all have to be stable over all all following processing steps or if one can, e.g., change the name