Re: [Freesurfer] occipital lobe WM errors

Hey Bruce. I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usuall

Re: [Freesurfer] Determining problems for subjects using recon-all.log

Hi Vy Was there an error? I just looked at the first one and it ended with no error. Try running recon-all -make all and see if it completes Cheers Bruce > On Jul 28, 2014, at 4:36 PM, Vy Dinh wrote: > > Dear Freesurfer develops, > > I'm having issues running recon-all -all on 2 of our subjec

Re: [Freesurfer] occipital lobe WM errors

Hi Matt there are instructions on our wiki. You can either ftp or use the filedrop, although ftp is probably best if you are uploading an entire subject cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote: Hey Bruce. Thanks for the response. How do I go about uploading the subject? On Mon

Re: [Freesurfer] occipital lobe WM errors

Hey Bruce. Thanks for the response. How do I go about uploading the subject? On Monday, July 28, 2014, Bruce Fischl wrote: > Hi Matt > > certainly something is wrong, but it's hard to tell why from the single > slice. You have big topological defects that are being fixed incorrectly. > Can you

Re: [Freesurfer] preserve manual edits?

Got it. Thanks Bruce. On Mon, Jul 28, 2014 at 11:18 AM, Bruce Fischl wrote: > phew. Then you should be able to copy those over to your new runs if you > want (that is, copy all the 1s and 255s into the volumes in the new > directories). I assume you are rerunning recon-all from scratch? Or you

Re: [Freesurfer] occipital lobe WM errors

Hi Matt certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote: Hello Freesurfer team, I've us

[Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

Dear FreeSurfer experts, Bruce/Doug, I am running my analysis on a server. I have a total of 128 GB RAM, when I run my analysis and when it stops I'm consuming ~44, having about 83 free. I can run 1224 subjects but no more than that. As soon as I have 1225 subjects the analysis won't run (but

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

Thanks Doug -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 28, 2014 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum white matter mask {Disarmed

Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

Does mri_mask work? On 07/28/2014 12:50 PM, Bastian Cheng wrote: > Thank you, Douglas! > > Is there a way to mask my functional ROI with these binarized aparc ROIs? > > I guess what I want to do is: ROIfunctional * > ROI_precentral_binarized > masked ROIfunctional limted to precentral > region >

Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

Thank you, Douglas! Is there a way to mask my functional ROI with these binarized aparc ROIs? I guess what I want to do is: ROIfunctional * ROI_precentral_binarized > masked ROIfunctional limted to precentral region best regards, Bastian. On 28 July 2014 18:25, Douglas N Greve wrote: > > Try

Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the same ROIs as aparc but in volume format). You can map this into your functional space. doug On 07/25/2014 06:29 AM, Bastian Cheng wrote: > Dear Freesurfers, > > Is there a way to mask a custom ROI (or label) with a volume /

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

I can't make anything out of the error msg gif. Somewhere in there, there should be a mris_preproc command line. Can you try cutting and pasting that into a shell? Trying to do this in the context of qdec will be difficult doug On 07/25/2014 05:09 AM, Isotalus, Hanna wrote: > > Dear FreeSurfer

Re: [Freesurfer] Converting volume to label

I'm getting back to my emails but I'm not sure where this thread is ... doug On 07/23/2014 02:05 PM, Bruce Fischl wrote: > if it's in alignment without the .dat file you probably shouldn't use the > dat file in the sampling onto the surface. I don't think it was created > by recon-all though > >

[Freesurfer] Permutation testing in freesurfer

Hello all, Does anyone know of a toolbox/script that would automate permutation testing in freesurfer? For example running x number of random permutations of a covariate and recording max sig levels similar to what the software SnPM does for SPM analyses? Thanks. -Andrew

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

With mri_binarize you can give it multiple match options to merge different segments On 07/28/2014 11:50 AM, Alshikho, Mohamad J. wrote: > Hi Bruce, > Thank you very much for your quick answer, > The output of those command lines are left and right cerebellum white matter. > How can I create a

Re: [Freesurfer] Permutation testing in freesurfer

This is build into mri_glmfit-sim. Run it with --help to get more info doug On 07/28/2014 11:54 AM, O'Shea,Andrew wrote: > Hello all, > Does anyone know of a toolbox/script that would automate permutation > testing in freesurfer? For example running x number of random > permutations of a covariat

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Bruce, Thank you very much for your quick answer, The output of those command lines are left and right cerebellum white matter. How can I create a mask for the whole cerebellum white matter? Thanks Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] LocalGI error

Hi Sarina, Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject? Thanks, Marie On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" mailto:sarina.iwabu...@nottingham.ac.uk>> wrote: Hi all, I have been trying to run localGI and have been coming across errors. It

Re: [Freesurfer] preserve manual edits?

phew. Then you should be able to copy those over to your new runs if you want (that is, copy all the 1s and 255s into the volumes in the new directories). I assume you are rerunning recon-all from scratch? Or you could just copy the whole directory, and rerun recon-all -all on the new directory

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Mohamad you can use mri_binarize --match or mri_extract_label on the aseg.mgz. cheers Bruce On Mon, 28 Jul 2014, Alshikho, Mohamad J. wrote: Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks  moha

[Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis

[Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter

Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundari

Re: [Freesurfer] preserve manual edits?

Hi Bruce, Used v5.3 for original edits using the "recon" mode in freeview so edits used 1 for "off" and 255 for "on". Jason On Mon, Jul 28, 2014 at 9:22 AM, Bruce Fischl wrote: > Hi Jason > > what version? Did it support recon mode? The edits need to use 1 for "off" > and 255 for "on", otherwi

[Freesurfer] LocalGI error

Hi all, I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors: >> reading filled volume... set: Variable name must begin with a letter. gunzip: Command not found. ERR

Re: [Freesurfer] preserve manual edits?

Hi Jason what version? Did it support recon mode? The edits need to use 1 for "off" and 255 for "on", otherwise we can't track them. cheers Bruce On Mon, 28 Jul 2014, Jason Tourville wrote: Hi Bruce,I used Freeview to edit the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes

Re: [Freesurfer] preserve manual edits?

Hi Bruce, I used Freeview to edit the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes. Cheers, Jason On Fri, Jul 25, 2014 at 9:23 PM, Bruce Fischl wrote: > Hi Jason. > How were the edits done? > Cheers > Bruce > > > On Jul 25, 2014, at 10:40 AM, Jason Tourville wrote: > > > >

Re: [Freesurfer] Freesurfer ROI analysis

Hi Silas are the two scans at the same time point? It really depends what your hypothesis is. Certainly start with a cross-sectional analysis, as you need to anyway. And yes, you are correct - it is usually better to pick the better scan than use both if one of them is corrupted cheers Bruce

Re: [Freesurfer] Freesurfer ROI analysis

Hi Bruce, Thanks for your help! But - would you recommend a longitudinal analysis even though i have quite many movement artefacts and bad scans - instead of just avoid using the worst picture? At the moment I'm making a cross-sectional study. I would also like to make an investigation of OFC gr