Re: [Freesurfer] question about total gray matter volume.

I think that will work. doug On 1/13/12 7:17 PM, Mehul Sampat wrote: Hi Folks, I saw that mri_segstats from v5.0 onwards has an option to measure the total gray matter volume (--totalgray). My question is, If I have dataset processed with FS v4.5, can I use the mri_segstats (from v5.0) to me

Re: [Freesurfer] Fwd: matlab: No MATLAB bin directory for this machine architecture.

Hi Kiley, the problem is with your matlab setup. As you point out your matlab is 32 bit but your machine is 64 bit. This should be able to run, but I don't know how to modify the matlab install to make it run. If you can, try to upgrade to the 64bit version. doug On 1/13/12 1:48 PM, Kiley wr

[Freesurfer] question about total gray matter volume.

Hi Folks, I saw that mri_segstats from v5.0 onwards has an option to measure the total gray matter volume (--totalgray). My question is, If I have dataset processed with FS v4.5, can I use the mri_segstats (from v5.0) to measure the total gray matter volume on this dataset ? Thanks Mehul ___

Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask

Can you please test [recon-all -all -clean-bm -s subjid] with one of your subjects in 5.1 (with brain.finalsurfs.manedit.mgz in your subject's mri directory)? If it does work, then at least we can rule out that version 5.1 does not have a bug and I can troubleshoot on my end. If that does not wo

Re: [Freesurfer] overlay alignment in tkmedit

Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead: mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug Anthon

Re: [Freesurfer] overlay alignment in tkmedit

what does mri_info say about them (and the rawavg.mgz) On Fri, 13 Jan 2012, Anthony Dick wrote: > It was created from the ahuman_1_do_shft.nii volume, which was what was > input to recon-all in Freesurfer. And these volumes (the overlay and > underlay) align in other viewers (e.g., AFNI and mricr

Re: [Freesurfer] overlay alignment in tkmedit

It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron). On 1/13/12 2:40 PM, Douglas N Greve wrote: > What volume was human_1_do_shft.nii created from? >

Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask

Haven't noticed it but maybe we missed something. I'd like to look at your case if I can to try to figure it out. If you'd rather not send the case, I'll try some testing on this end to see if I can replicate it. On Fri, 13 Jan 2012, Vy Dinh wrote: > Hi Allison, > > Upon a closer look, it appea

Re: [Freesurfer] FA and non_FA group analysis

If Class1>Class2, then the voxel will be red, otherwise it will be blue. Or am I misunderstanding your question? Antonella Kis wrote: > Hi Doug, > > Many thanks again for your valuable support. > > I have one more question please how I know which case I have > Class1>Class2 or Class2>Class1? > >

Re: [Freesurfer] FA and non_FA group analysis

Hi Antonelle, the way you have have it set up, C = [+1 -1] will be positive (red) for Class1>Class2 and negative (blue) for Class2>Class1. Your fsgd file looks ok. doug Antonella Kis wrote: > Hi Doug and many thanks for your reply and help. If blue means neg, > red/yellow is positive does this

Re: [Freesurfer] FA and non_FA group analysis

Hi Doug and many thanks for your reply and help. If blue means neg, red/yellow is positive does this means that where is blue we have a decrease in FA for while positive means an increase? How I know if there is a decrease in controls versus patients and not opposite (FA decreases in patients

Re: [Freesurfer] overlay alignment in tkmedit

What volume was human_1_do_shft.nii created from? Anthony Dick wrote: > Here is the command, in case I didn't run it right. > > adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz > chuman_1_do_shft_new.nii > mri_convert chuman_1_do_shft.nii --in_like orig.mgz > chuman_1_do_shft_new.nii

Re: [Freesurfer] Selxavg3-sess Out of Memory - What are the options?

Hi Shahin, you actually can do this in 5.x. If you configure the analysis correctly, you can analyze in the native functional space. Part of 5.x will require that you have a subject, but that subject can be anything (eg, human fsaverage), and, if you configure for native space, the results that

Re: [Freesurfer] selxavg3-sess issue in FSFAST

Hi Ivan, can you send me verbgen.sm5.lh/analysis.info? doug Ivan Alvarez wrote: > Dear Freesurfers, > > I recently attempted my first FSFAST analysis following the tutorial > on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt > while usin

Re: [Freesurfer] overlay alignment in tkmedit

Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug Anthony Dick wrote: > Good question. The parcellation is created outside of Freesurfer (the > data were shared from another lab and I don't kn

Re: [Freesurfer] Fwd: matlab: No MATLAB bin directory for this machine architecture.

Hi Kiley, you should not have to change anything. matlab just needs to be in your path. When you open a terminal and type: which matlab what do you get? doug Kiley wrote: > > > Begin forwarded message: > >> *From: *Kiley > > >> *Date: *January 13, 2012 1:17:04 P

Re: [Freesurfer] overlay alignment in tkmedit

Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.

Re: [Freesurfer] Fw: FA and non_FA group analysis

Look at the original sig map. This will be signed (blue and red/yellow), with blue being neg, red/yellow being positive. doug Antonella Kis wrote: > Dear Doug, > > I am forwarding Bruce answer to my question since he directed me to you. > > I need some help regarding my FA and non-FA group analys

[Freesurfer] FA and non_FA group analysis

Dear Doug, I need some help regarding my FA and non-FA group analysis study. I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register.  I used the GLM group analysis method after I concatenate FA from individuals i

Re: [Freesurfer] overlay alignment in tkmedit

Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug Anthony Dick wrote: > Hello, > > I am trying to train a cerebellar atlas based on 20 manually parcellated > cerebellums. I have run the anatomical through freesurfer. When I try to > load the overlay

Re: [Freesurfer] dcmunpack bug for unconsolidated dicoms

Hi Steve, if the same volume is distributed over multiple directories, then it will surely fail (actually, it is mri_convert that assumes that all files for a given volume will be in the same directory). I don't know of anyone else who has had this problem, even those who are scanning for 20 mi

[Freesurfer] Fwd: matlab: No MATLAB bin directory for this machine architecture.

Begin forwarded message: > From: Kiley > Date: January 13, 2012 1:17:04 PM GMT+01:00 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: matlab: No MATLAB bin directory for this machine architecture. > > Hi Freesurfers > > I have just begun using Freesurfer (and the mac terminal) to do my >

[Freesurfer] overlay alignment in tkmedit

Hello, I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignme

[Freesurfer] dcmunpack bug for unconsolidated dicoms

There is a bug in the new *dcmunpack* that replaces the earlier * unpacksdcmdir* when it is unpacking a "fragmented" dicom directory, i.e. one in which the files were saved to DVD incrementally during the scan, as opposed to dicom files that are saved all at once, after all the scanning is complete

Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask

Hi Allison, Upon a closer look, it appears that there were still some corrections to be made for the subject whose 5.0 corrections "were preserved," just not as many edits for this subject as the others. (The difference in the amount of edits we need to make were significant, however.) For one

Re: [Freesurfer] Performance questions

Hi Malcolm in collaboration with IBM we are also looking at MPI and pthreads. cheers Bruce On Fri, 13 Jan 2012, Malcolm Tobias wrote: > > Is there a standard benchmark for FreeSurfer? > I've been using the data under subjects (Bert?/Ernie?) and running a recon- > all: > > recon-all -s ernie -i

[Freesurfer] Performance questions

Is there a standard benchmark for FreeSurfer? I've been using the data under subjects (Bert?/Ernie?) and running a recon- all: recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz -all On our hardware using the 5.1 distributed binary (freesurfer-Linux- centos4_x86_64-stable-pub-v5.1.0.tar

[Freesurfer] manually labeled brains for segmentation atlas

Dear Freesurfer specialists, I'm currently working on a comparison between manual segmentations and freesurfer segmentations of the hippocampus. Therefore i would be very interested in the atlas used for subcortical segmentation. On the wiki i read that the manually labeled brains used to build