[Freesurfer] interpretation of qdec results

Dear FS experts,
I use qdec to do two group study. in QDEC, it set Normal = 1 and Disease = 2, use AGE as covariate and apply DODS model, after analyze group cortical thickness, it showed significant negative T value (blue color) in some brain areas. I have two questions in qd

Re: [Freesurfer] recon-all -s exited with ERRORS

Thanks a lot, it works. just waiting 24 hours. Best regards, Carolina 2011/6/10 > Hi Carolina, > > Sorry My bad. I was inaccurate in my previous message. > > -subject should work. > > Assuming that the MPRAGE of your subject is under the following directory: > > /freesurfer/subjects/buckner_da

Re: [Freesurfer] aseg labels 96 and 97

Hi Andy, I don't think that we ever labeled those regions. Or did you do these by hand? If you have a label that you want to see the code for, you can load it into tkmedit like tkmedit subject orig.mgz -aux aseg.mgz -aseg when you click on a label, you can see its number in the aux value. doug

Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

Do you mean your individual subject after running through FS has a file called t1.mgz and not T1.mgz? Something is definitely wrong there. Can you send the log file? doug t...@ms36.hinet.net wrote: > > Dear FS experts, > I use FS5.1 and previous data run on other machine. When I try to > make_aver

Re: [Freesurfer] A question about the coords of the vertex

They are in our own coordinate system, documented on our wiki. Do a search for coordinates to find the page. doug soft.join Huang wrote: > Hi all, > > I have a question about the coords of vertex in ?h.white file. > I load the ?h.white file in Matlab and get a variable called > vertex_coords,

Re: [Freesurfer] qustions about contents of label file

That interpretation is correct. The MNI coords are MNI305. The last field is to hold a statistic. If it is 0, it means that the field was not filled with anything. doug ZhiLiangLong wrote: Hello: I use qdec to generate statistical significant areas and draw ROI and map the ROI to each subject

Re: [Freesurfer] Whole brain parcellation.

Anything that is non-0 will cover the whole brain. doug Sudhin A. Shah wrote: > Hi, thank you. Is there a range in the labels that will ensure that I am > including the whole brain? I.e. I see labels for Cx, but not subcortical.. > If I take labels 1001 to 2001 ( for eg ) will that cover whole br

[Freesurfer] trac-all - bedp errors

Dear Tracula Users I completed trac-all -prep -c without difficulty or errors. However, without any changes to my director structure or my Tracula config file I am receiving the following errors when running trac-all -bedp -c. I will copy and past my config file contents below the error messages.

Re: [Freesurfer] trac-all - bedp errors

Hi Deryk, Is bedpostx properly installed in your computer? Can you just type bedpostx in your terminal to see if it gives this message? Usage: bedpostx [options] expects to find bvals and bvecs in subject directory exp

Re: [Freesurfer] trac-all - bedp errors

Hi Priti Thank you for your quick replay. The following files / folders are listed in my dmri.bedpostx directory: ** /usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls commands.txt diff_slices logs monitor xfms ***

Re: [Freesurfer] trac-all - bedp errors

Hi Priti In addition, if I run bedpostx from the command line as follows: bedpostx /usr/local/freesurfer/subjects/C001/dmri it works just fine without errors. Deryk Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO Speech-Language Pathologist C.I.H.R. Post Doctoral Research Fellow Department

Re: [Freesurfer] pet partial volume correction

A couple of things: Map aparc+aseg into the PET space: mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp subject.pet.pvf.nii --o subject_bl.petlabel.nii Use the PET space aparc+aseg when computing the seg stats: mri_segstats --seg subject_bl.petlabel.nii --sum /home/corinna/blstats/s

[Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

Hello Freesurfers, I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These masks are .nii files, and have a RAS orientation. I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matchi

Re: [Freesurfer] Whole brain parcellation.

Hi Sorry for bothering you again, but I am not sure I understand. I was running whole brain correlation analysis (voxel by voxel). BUT for comparison purposes, I want to compute region by region correlation matrix. So, I want to divide up the brain into freesurfer parcellated regions - i.e. with

[Freesurfer] Pulvinar Segmentation

Hi, I'm interested in pulling out segmentation stats on the Pulvinar. I noticed that Pulvinar is listed in the FreeSurferColorLUT.txt but isn't in the aseg.stats. Is there a way to get segmentation information for the Pulvinar? best, Peter ___ Fre

Re: [Freesurfer] recon-all -s exited with ERRORS

Hi Carolina, Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda? Thanks, *Leo Souza* On 06/13/2011 07:04 AM, Carolina Valencia wrote: Thanks a lot, it works. just waiting 24 hours. Best regards, Carolina 2011/6/10

Re: [Freesurfer] recon-all -s exited with ERRORS

When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account. doug Leo Souza wrote: > Hi Carolina, > > Do you know how can

Re: [Freesurfer] recon-all -s exited with ERRORS

Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers. Thanks, *Leo Souza* On 06/13/2011 02:44 PM, Douglas N Greve wrote: When you run recon-a

Re: [Freesurfer] recon-all -s exited with ERRORS

Sorry my typos, got a weird keyboard here. Thanks, *Leo Souza* On 06/13/2011 03:27 PM, Leo Souza wrote: Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if youŕe using any r

Re: [Freesurfer] recon-all -s exited with ERRORS

Try adding -use-cuda to recon-all Leo Souza wrote: > Yes, I did that, but it doesn't actually uses the GPU to do that, only > CPU. > > GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q > -d UTILIZATION -l 3" if your'e using any recent drivers. > > > Thanks, > *Leo Souza* > >

[Freesurfer] Adding a new measure to the design tab

Hi, So I'm trying to add new measures, after having run recon-all -qcache, to my design tab drop-down menu and it doesn't seem to be working. I was a little confused about the .Qdecrc file. I put a file named qdec.Qdecrc file inside my $SUBJECTS_DIR/qdec/ and i also have a qdec.fsgd file in the

Re: [Freesurfer] recon-all -s exited with ERRORS

Okay, Let me see what's gonna happen. Thanks, *Leo Souza* On 06/13/2011 04:10 PM, Douglas N Greve wrote: Try adding -use-cuda to recon-all Leo Souza wrote: Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvi

Re: [Freesurfer] trac-all - bedp errors

Hi Deryk - Trac-all doesn't call the version of bedpostx under the FSL dir but a specially modified version in the freesurfer distribution (called bedpostx_seychelles for historical reasons). It's fine to run bedpostx directly since that works for you. You can also upload the data set for us

Re: [Freesurfer] Tracula question: trac-all config file and number of B0 specification

No, if usemaskanat = 1, then the diffusion mask that comes from applying bet to the lowb volume will not be used for tractography. A dilated version of aparc+aseg will be used as a mask instead, which is typically more reliable than trying to find the right bet threshold. On Fri, 10 Jun 2011

Re: [Freesurfer] recon-all -s exited with ERRORS

-use-cuda is invalid I think, but I did -use-gpu and see what I get: [root@cuda-final2 bin]# ./recon-all -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0

Re: [Freesurfer] Pulvinar Segmentation

no, sorry, not yet. Maybe in a year or two! Bruce On Mon, 13 Jun 2011, Peter J. Molfese wrote: > Hi, > > I'm interested in pulling out segmentation stats on the Pulvinar. I noticed > that Pulvinar is listed in the FreeSurferColorLUT.txt but isn't in the > aseg.stats. Is there a way to get seg

Re: [Freesurfer] recon-all -s exited with ERRORS

recon-all -s bert -all -use-gpu -- iOS 4.3 Em 13/06/2011, às 21:30, Leo Souza escreveu: /recon-all -use-gpu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] recon-all -s exited with ERRORS

How long does it take to run the test? Thanks, Leo Souza From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br] Sent: Monday, June 13, 2011 6:20 PM To: Leo Souza Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -s exited with ERRORS recon-all -s bert