Re: [Freesurfer] Mac Pro with 12cores

You can run 12 recon-all in parallel. You'll have 12 patients processed in each day approximately - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile

[Freesurfer] about recon-all command

Hello All, I have a question about recon-all command with "-cw256" option. What is the difference between "recon-all" and "recon-all with -cw256"? What is "-cw256 option"? When I tried executing recon-all command, I had an error message: / // ERROR! FOV=32

Re: [Freesurfer] about recon-all command

That flag is needed if your input is larger than the required size by FreeSurfer 256x256x256. You would not use it on input that did not require it (ie it is smaller than 256x256x256). On Mar 10, 2011, at 4:53 AM, Kenichiro Tanaka wrote: > Hello All, > > I have a question about recon-all co

Re: [Freesurfer] Mac Pro with 12cores

If you have enough memory! Maybe Richard can post current CPU recon times with the latest hardware and optimizations. I think they are much shorter than they used to be On Mar 10, 2011, at 3:28 AM, Pedro Paulo de Magalhães Oliveira Junior wrote: > You can run 12 recon-all in parallel. > > Y

Re: [Freesurfer] Small voxel size

Hi Tricia, I don't think you can use that subject. It will only have 39% of the SNR of the others. Sorry :< Bruce On Wed, 9 Mar 2011, Tricia Merkley wrote: The native resolution of the other subjects is (1,1,1)mm voxel size and (256,256,160) voxels, whereas this subject is (0.7,0.7,0.8) mm

Re: [Freesurfer] Mac Pro with 12cores

On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote: > If you have enough memory! Maybe Richard can post current CPU recon > times with the latest hardware and optimizations. I think they are > much shorter than they used to be My workstation (3.2 GHz Nehalem) can do a recon-all ernie in about

Re: [Freesurfer] Mac Pro with 12cores

That's without GPU? On Thu, Mar 10, 2011 at 11:17, Richard G. Edgar wrote: > > On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote: > > If you have enough memory! Maybe Richard can post current CPU recon > > times with the latest hardware and optimizations. I think they are > > much shorter th

Re: [Freesurfer] Mac Pro with 12cores

On Thu, 2011-03-10 at 11:29 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: > That's without GPU? Yes. CPU only stream. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] mri_glmfit allocate memory error

There appears to be something wrong with the lh.paired-diff.thickness.mgh file. How was it created? doug Andrew Mendlowitz wrote: > Hello All, > I get the following error while trying to run mri_glmfit. I am running > a 2.93 > ghz imac with 8gb of ram. I am also running freesurfer version 5.0.0

Re: [Freesurfer] DODS and DOSS

Hi Chris, If you run an ANCOVA model with an interaction (which is what DODS is) then the interpretation of the group effect is ambiguous because the "group" effect varies with age. If there is actually a differential slope between groups, then the p-value of the contrast of the group means (i.e.

[Freesurfer] mri_glmfit-sim error

hi folks, when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg i get an error message ERROR: cannot find /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd there is fsaverage... should i just make a soft link ? also when i

Re: [Freesurfer] mri_glmfit-sim error

You can make a soft link. Don't worry about that warning (it's not important, and I've fixed it for the next version). doug GREGORY R KIRK wrote: > hi folks, > > when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg > i get an error message ERROR: cannot find > /apps/x86_64

Re: [Freesurfer] Small voxel size

OK, thanks so much for letting me know.  Any idea how it might affect cortical thickness or subcortical volume results (over-estimation/under-estimation)? We do try to use the same image acquisition parameters for all subjects in a given study of course, but this was an unusual case... Thanks,

Re: [Freesurfer] Small voxel size

not sure. They will be less accurate I would think On Thu, 10 Mar 2011, Tricia Merkley wrote: OK, thanks so much for letting me know.  Any idea how it might affect cortical thickness or subcortical volume results (over-estimation/under-estimation)? We do try to use the same image acquisition

[Freesurfer] Newbie - Group analysis on a single session with multiple runs.

Hi All, We are trying to speed things up in our functional analysis pipeline, and I wanted to consult with the experts here about the following suggestion... At the moment, we typically collect multiple runs per subject (say, 10-20). We usually then run pre-processing on each run, and then do fir

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

Are you using FSFAST? It does not load all the data into memory, only one at a time. It does make sense to do an individual run analysis (assuming you have all conditions in each one). You can run selxavg3-sess with the -per-run option. The higher level analysis is going to be a little bit tric

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

Hi Doug, Yes. I am using FSFAST for the analysis, and I do have all conditions in each run. Can you elaborate more why the higher level analysis is going to be tricky? What is wrong with loading the beta regressors from each run and building the contrast by averaging same beta regressors from diff

[Freesurfer] Reconchecker error

Hi all - I am trying to run the reconchecker program to get some QA done on my data and I get the below error. Any help on this would be greatly appreciated! Also are there any other QA programs that would enable me to easily visualize the outputs at various stages of Freesurfer recon-all?

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

That is a fine thing to do, I just don't have dedicated code to do it (ie, you can't run isxconcat-sess on them). But if you want to do it on your own, it will work fine. doug Shay Ohayon wrote: > Hi Doug, > > Yes. I am using FSFAST for the analysis, and I do have all conditions > in each run.

[Freesurfer] extracting thickness values from group level map

Hi Surfers! I have done a group level analysis relating a variable to thickness values. I have a sig.mgh file that shows the relationship between the variable and thickness at each vertex. Now I would like to threshold the sig.mgh file (at values of 3 and above), and then extract an average thic

Re: [Freesurfer] extracting thickness values from group level map

You're almost there, Beth. When you run mri_surfcluster, specify the --ocn output. This will create a 'segmentation' with each value being the number of the cluster. Then use mri_segstats specifying the ocn as the segmentation and the cluster number you want as the segid. Also specify and outp

[Freesurfer] effect size for cortical thickness changes

Hello All, Are there reports of studies of cortical thickness changes using freesurfer which report effect sizes for the ROIs of interest ie how much of a change in millimeters was observed as opposed to p-values reported. Please let me know. Thanks a lot Ri __