[Freesurfer] recon-all and local Gyrification Index

Hello, I ran several recon-all processes on raw T1 MRI data. I was trying to run recon-all -lgi as per the instructions from this paper - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/ but it fails with an error that Matlab is required. So, my question is if local GI is already computed by

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, Thank you so much for assistant me in the process. I could do that. It worked. Thanks Faezeh Vedaei On Wed, Mar 2, 2016 at 6:15 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your help. I just got your meaning. I created new > LUT file by just changing

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

On 3 March 2016 at 13:22, Francis Tyson Thomas wrote: > Also, it looks like development for GPU usage has been halted for now and so > I was trying to use the CUDA 5 for getting it working under ubuntu 14.04. I > have been not successful that as the cuda device

Re: [Freesurfer] conflicting Monte Carlo simulation results...

yes, that is the right file On 03/03/2016 02:20 PM, Karl Liu wrote: > Dear Doug, > Thank you for your clarification. It sounds the right way for > correction is: > > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ > --cwp 0.05\ --2spaces > > > > One last question: Is the

Re: [Freesurfer] error in mc-sess

On 03/03/2016 02:46 PM, Ji Won Bang wrote: > Thanks for your reply. It works. > > I have 1 more general question. > > When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 > > I get 2 files (template.log & template.nii.gz) under the functional > subdirectory(bold_day1) and

Re: [Freesurfer] error in mc-sess

Thanks for your reply. It works. I have 1 more general question. When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 I get 2 files (template.log & template.nii.gz) under the functional subdirectory(bold_day1) and under each run(001, 002 etc). When I run: mc-sess -s

Re: [Freesurfer] conflicting Monte Carlo simulation results...

Dear Doug, Thank you for your clarification. It sounds the right way for correction is:mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces One last question: Is the resulting "cache.th40.neg.sig.cluster.summary" the right file to look for post-correction

Re: [Freesurfer] AAL atlas question

Hi Doug, Thanks for your response! Panos > I would recon the mni152 (or whatever space the AAL atlas is in), map > the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to > transfer them to the individual. > > On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS

[Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

Hi, I have been working on speeding up the the hippocampal segmentation in freesurfer 6 beta and I have been playing around with both -openmp and -use-gpu flags. I noticed that freesurfer does seem to make use of all the threads in freesurfer 6 irrespective of passing the -openmp flag or not. Is

Re: [Freesurfer] Qdec-statistical map

yes On 03/03/2016 01:06 PM, John Anderson wrote: > This si Great!!! Thanks Doug. One more question: > What is the correct input in the command mri_surfcluster. Is it the > image "sig.mgh" ? > > Bests, > John > *Sent:* Thursday, March 03, 2016 at 12:47 PM > *From:* "Douglas N Greve"

Re: [Freesurfer] Qdec-statistical map

This si Great!!! Thanks Doug. One more question: What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?     Bests, John    Sent: Thursday, March 03, 2016 at 12:47 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] "wm" boundaries and stats

Thanks very much, Doug. I could always hope. > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, March 03, 2016 12:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re:

Re: [Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

If it affects anything, it would only affect the BA labels. If the BA labels did not change between 5.1 and 5.3, I don't think it would affect anything. On 03/03/2016 12:41 PM, Adam Martersteck wrote: > Hi Freesurfer team, > > *Short question: *Will (accidentally) using the fsaverage v5.3

Re: [Freesurfer] Qdec-statistical map

You will have to extract clusters (mri_surfcluster) to create an annotation, then use mri_segstats with the --annot option and specifying the y.mgh file as input and the output using something like --avgwf output.txt (also add --exludeid 0). The output will have a row for each frame in y.mgh

Re: [Freesurfer] "wm" boundaries and stats

Hi Don, there is not an easy way to get this information. You can use mri_binarize to create a surface of each ROI, something like mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual Use this version of mri_binarize

Re: [Freesurfer] Qdec-statistical map

Hi Doug, How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject?   Bests, John    Sent: Thursday, March 03, 2016 at 12:37 PM From: "Douglas N Greve"

[Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

Hi Freesurfer team, *Short question: *Will (accidentally) using the fsaverage v5.3 subject in our v5.1 directory influence our reconstructions? *Long question:* Our server has 2 different freesurfer environments. A recon was accidentally run on a single v5.1 subject in the v5.1 directory with

Re: [Freesurfer] error in mc-sess

what is your command line? You have to use -per-run and not -per-session On 03/03/2016 12:22 PM, Ji Won Bang wrote: > Dear. freesurfer experts. > > Hi. I'm using freesurfer version 5.3.0. > > I tried mc-sess onto runs that have different number of slices. > > However, due to this different number

Re: [Freesurfer] Permission denied error with mri_surfcluster command

All the values are between 0 and 1, so I suspect this is a map of p-values, not a map of -log10(p). Is that right? If so, convert it to -log10(p) and rerun. You can do this in matlab with p = MRIread('rh_time.mgh'); sig = p; sig.vol = -log10(abs(p.vol)); MRIwrite(sig,'sig.mgh'); On 03/03/2016

Re: [Freesurfer] Qdec-statistical map

not sure what you mean. the statistical map will have a single value, not a value for each subject On 03/03/2016 12:31 PM, John Anderson wrote: > Dear FS experts, > I am using Qdec to study the differnce in cortical thicnkess between > two groups. > Qdec is running a GLM analysis. This will

Re: [Freesurfer] error in mc-sess

you have to use -per-run not -per-session On 03/03/2016 12:27 PM, Ji Won Bang wrote: > The command I used is: > > mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session > > Thank you. > > Best, > Ji Won > > > >

Re: [Freesurfer] conflicting Monte Carlo simulation results...

In the first command you only used 5 samples in your simulation. If you read the "Notes" section below the command, you'll see that this should be something like 5000. Only 5 was used because it would take very long to run. In general, you don't need to run the simulation because it has

[Freesurfer] Qdec-statistical map

Dear FS experts, I am using Qdec to study the differnce in cortical thicnkess between two groups. Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess. How can I extract the numbers of cortical thickness for

Re: [Freesurfer] Problem with mriconvert

Do you have write permission to that folder? Is the disk full? On 03/02/2016 11:12 AM, Óscar Soto Angona wrote: > Hello, > > We are medicine students who are using freesurfer for research. We had > been using freesurfer in Ubuntu 12.02 without encountering any > trouble; recently we updated to

Re: [Freesurfer] error in mc-sess

The command I used is: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session Thank you. Best, Ji Won 2016-03-03 12:22 GMT-05:00 Ji Won Bang : > Dear. freesurfer experts. > > Hi. I'm using

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Can you send me rh_time_spval.mgh? On 03/01/2016 04:42 PM, Jennifer Legault wrote: > Hi Doug, > > Thank you for responding. I actually realized what was the matter (I > had specified the path for fsaverage which led to the error; this is > no longer an issue so long as I use "--subject

[Freesurfer] error in mc-sess

Dear. freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried mc-sess onto runs that have different number of slices. However, due to this different number of slices in different runs, mc-sess gives an error. I expected that running mc-sess in freesurfer version 5.3.0 would handle

Re: [Freesurfer] How to find the difference between to different fMRI datasets?

Create a contrast between the two conditions On 03/01/2016 01:27 AM, Silas wrote: > > Dear FreeSurfer team, > > > Thank you for all your help so far! > > > I would like to visualize the difference between two fMRI data sets. > > Data set1: Cortical activation during movement of a finger. > > Data

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

I cannot replicate the error. What version of FS are you using? What happens if you run mri_glmfit --fsgd RPA-acc.fsgd or mri_glmfit --fsgd RPA-accGT.fsgd On 02/29/2016 09:38 PM, Joseph Dien wrote: > Hi, > I’m having an fsgd error that has totally stumped me. I’m trying to run > the

Re: [Freesurfer] AAL atlas question

I would recon the mni152 (or whatever space the AAL atlas is in), map the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to transfer them to the individual. On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS community, > > I have recon-ed a set of subjects and I

Re: [Freesurfer] Extract LGI at MaxVertex and extract effect-sizes in table format

On 02/29/2016 02:38 AM, Bittner, Nora wrote: > > Dear FreeSurfer Experts, > > Sorry for reposting this massage again, but I still have two > questions, which you can hopefully answer to: > > 1) > > I calculated several analyses with LGI as my dependent variable, > resulting in several

Re: [Freesurfer] Reading values from overlays with PETcoreg

No, not yet, though I recently had a need to do the same thing. It is pretty easy to do though. If you run mri_gtmpvc with --save-input, it will create a file called input.rescaled.nii.gz. Then you can run mri_segstats --i input.rescaled.nii.gz --seg aux/seg.nii.gz --ctab aux/seg.ctab

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

Sorry, I'm still having a problem following what you are trying to do. You have a 3x3 functional design (3 levels of reward, 3 levels of risk), and you want to look for an interaction between reward and risk? On 02/24/2016 12:10 PM, Afzal, Afsana wrote: > Hi Doug, > > Upon reviewing the