[Freesurfer] FreeSurfer stable v.6 Installation

Dear FreeSurfer experts I would like to ask that whether or not I can install the package to the existing FS 5.3 that previously installed on our Linux system? Please forgive if it is an obvious question. Thanks *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC*

Re: [Freesurfer] Volume maps unit in FreeView

Thanks Dr. Greve. That makes sense if the color bar in FreeView represents vertex-wise volume and area for ?h.volume and ?h.area respectively. Actually, 20-40K mm^3 (i.e. 20-40 cm^3) volume range I extracted is for Yeo networks, I guess thats why this range is much higher compared to vertex-wise

Re: [Freesurfer] mirroring right-hemisphere cluster dimensions on left hemisphere

It’s for a group, but I could say the fsaverage is for an individual. Will give xhemi a try. Thank you so much Doug! Best, Fred On 2/15/17, 6:11 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve"

Re: [Freesurfer] display SPM results on inflated surface?

If your results are on the MNI152, you can run the mni152 through freesurfer, then use mri_vol2surf to map the data to the surface then view it with freeview (or tksurfer). You should not confuse this with doing the fMRI analysis on the surface. You will not have the benefits of surface-based

Re: [Freesurfer] mirroring right-hemisphere cluster dimensions on left hemisphere

If this is for an individual, then run it through the xhemi processing stream https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi There are examples there on mapping a label across hemis On 02/15/2017 03:30 PM, Uquillas, Federico D'Oleire wrote: > Dear FreeSurfer community, > > We have a cluster

Re: [Freesurfer] recon-all exited with ERRORS

What edits did you make to it? Can you check the T1.mgz to see if it looks ok? On 02/15/2017 07:56 AM, Dayanne Ferreira Ayres wrote: > Good morning, I tried to process a patient with the command below > after editing it: > > Recon-all-all -sd / Applications / freesurfer / subjects

Re: [Freesurfer] Fw: Re: bbregister

You don't need to do the bbregister or tkregister steps if the FS results are based on the T1.nii image as input. You can just use mri_vol2vol with --regheader instead of --reg t1.reg.dat (but the results should be about the same). For the problem, does aparc+aseg show up properly on the

Re: [Freesurfer] LGI error/Matlab/ a qestion for Douglas Greve

I think the ismac.m script was introduced in later versions of matlab. You can just create your own with the following content: function y=ismac y=0; return On 02/15/2017 01:59 PM, aral ahmadi wrote: > From: Douglas N Greve > So ismac.m is not defined in your matlab implementation? What

Re: [Freesurfer] Converting Surface Masks to Labels

You can also create an annotation from a group of labels (convert mask to label with mri_cor2label with the --surf option) using mris_label2annot (run with --help to get docs) On 02/15/2017 09:37 AM, Bruce Fischl wrote: > Hi Rita > > if you have labels you can just load them each in freeview

Re: [Freesurfer] Volume maps unit in FreeView

When you say volume maps, I assume you are talking about the ?h.volume file produced by FS. In that case (assuming you have not scaled the the eTIV), then that is "volume of a vertex" in mm3 (for surface area it is in mm2). Not sure what you mean about the actual volume values in the 20-40k

Re: [Freesurfer] cluster as ROI

Use something like this mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh --excludeid 0 --avgwf tp1.clustermean.dat The output tp1.clustermean.dat will be a matrix with nsubjects rows and nclusters columns where the value represents the mean for that subject in that

Re: [Freesurfer] Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir. On 02/14/2017 09:43 AM, West, John D. wrote: > > Hello. > > We are looking to save the interim subject files generated when > creating an fsaverage. These seem to be automatically deleted at

Re: [Freesurfer] Coordinates in different modality and space

On 02/13/2017 09:59 AM, Ting Qi wrote: > Dear freesurfer experts, > > I have some questions about the coordinates conversion, and the relationship > between several types of coordinates. > > First of all, I’d like to confirm whether the coordinates reported in the > results summary are based

Re: [Freesurfer] Normalization of external regressors

It depends a bit on whether they are nuisance regressors or not. If they are not nuisance regs, then I would be very careful normalizing them because it could make the regression coefficients hard to interpret when comparing across subjects (you would probably just use the same scale for all

Re: [Freesurfer] PET ROI analysis

This is a little tricky to do, but I can probably step you thru the process. The first thing you have to do is to transfer your ROI from fsaverage space to the individual using mri_label2label with the --regmethod surface option (view it on the surface to make sure it is ok). The next thing

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Hi Abby – Interesting, this means that it was the update and not the subject. I’ve never seen this issue before, and unfortunately these are all old builds that are hard to troubleshoot now. But if you want to send me one of the subject’s TRACULA directories, I can try to replicate the error on

Re: [Freesurfer] Freesurfer v6.0 / Developer version GPU implementation

Thanks Richard! I'll take a look at it and see how it turns up. On Mon, Feb 13, 2017 at 6:28 PM, R Edgar wrote: > On 13 February 2017 at 18:15, Francis Tyson Thomas > wrote: > > > I'm trying to reduce the freesurfer runtime as much as

Re: [Freesurfer] Intensity Re-scaling Relative to Full Brain Atlas

There is not a flag to do this, but it should be fairly easy. There will be a file called aux/global.gmwmcsf.dat. This has the mean value average over all GM, WM, and CSF voxels (after PVC). You can use this to scale your data like fscalc inputfile.nii.gz div value -o outputfile.nii.gz You can

[Freesurfer] bbregister

Thank you very much! Kindly, I have one follow up question:   I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth"  and I want to move it from native

Re: [Freesurfer] surface based PET analysis.

https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer On 02/15/2017 03:50 PM, miracle ozzoude wrote: > Hello Freesurfer, > I want to perform surface based PET analysis but I can't seem to find > a link for it. Please can someone direct it to me. Thanks. > Best, > Paul > > >

[Freesurfer] surface based PET analysis.

Hello Freesurfer, I want to perform surface based PET analysis but I can't seem to find a link for it. Please can someone direct it to me. Thanks. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] display SPM results on inflated surface?

Hi all, I was wondering if you knew of a way to display SPM results onto the inflated surface in Freesurfer. I have tried using SurfRend but there seem to be problems which might be due to the fact the results are obtained with SPM12 and SurfRend was designed to work with SPM5. Thanks, Lotte

[Freesurfer] Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.

Hi, My main question to the 6.0 experts is: Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white? Here's the reasoning behind this question. In previous

[Freesurfer] mirroring right-hemisphere cluster dimensions on left hemisphere

Dear FreeSurfer community, We have a cluster that we drew on the surface on the right hemisphere, and we’re interested in extracting cortical thickness values from the contralateral hemisphere. Wondering if there’s a way to transform the dimensions of our cluster from the right hemisphere to

Re: [Freesurfer] recon-all error

Hello Linette, You are getting the dreaded mri_nu_correct.mni correct. This error occurs when using freesurfer version 5.3 on newer linux platforms. This issue has been fixed in the latest release of freesurfer (v6.0) which I recommend you download and install.

Re: [Freesurfer] FS6.0, recon-all -parallel on OSX Sierra, dyld: Symbol not found: ___emutls_get_address

Hello Mira, I've only ever seen this error when installing version 6.0 on top of a preexisting freesurfer installation. Could you try completely removing the /Applications/freesurfer directory and reinstalling 6.0? If that doesn't work please upload the subjects folder and I will take a look.

[Freesurfer] recon-all when the input is the brain

Hello, If my input file of Freesurfer is the exacted brain.nii instead of T1 image T1.nii, how should I run recon-all? The brain has already been extracted and skull has been stripped by other softwares. Shall I run like the following: recon-all -noskullstrip -normneck -autorecon-all -subjid ID

Re: [Freesurfer] Fwd: LGI using Yeo Atlas

Hi Antonin and Thomas, Thanks a lot for your reply. I just wanted to confirm once again with you following steps. I ran: (1). mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh --sval-annot lh.Yeo2011_7Networks_N1000.annot --tval

[Freesurfer] LTA transforms into AFNI's aff12.1D format

Greetings, I am interested in using mri_robust_template to create an average anatomical image across several sessions (to which EPI runs will be aligned to). Are there any guidelines on how to convert the output .lta transforms into AFNI’s .aff12.1D format for later concatenation with the

[Freesurfer] Fwd: REMINDER Call for OHBM 2017 Replication Award

FYI Forwarded Message Subject:REMINDER Call for OHBM 2017 Replication Award Date: Wed, 15 Feb 2017 05:32:45 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu *REMINDER: Call for OHBM 2017

[Freesurfer] postdoctoral Research Fellow position at Mayo Clinic

The Department of Radiology at Mayo Clinic has an open position for a talented post-doc to work on a novel 3T MR scanner. The compact system sports 85mT/m gradients with slew rates in excess of 700T/m/s. DOI’s for a few papers on this system are: doi: 10.1002/mrm.26044 doi: 10.1118/1.4941362

[Freesurfer] REPOST: longitudinal QDEC cluster as ROI

Dear FreeSurfer Experts, I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that survives Monte Carlo correction. Now I would like to extract the data for each participant and each time point from that cluster so that I can plot the change. How could I do this? I tried

Re: [Freesurfer] tractstats2table error

This is of course a possibility but the script has been around for years, so it's been run with a range of versions. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Antonin Skoch [a...@ikem.cz] Sent: Wednesday,

Re: [Freesurfer] Converting Surface Masks to Labels

Hi Rita if you have labels you can just load them each in freeview and give them each a different color cheers Bruce On Tue, 14 Feb 2017, Rita Loiotile wrote: > Hi, > > I'm sorry for what seems like a trivial question. I couldn't find this > answer in the tutorials or old archive. > > I have

Re: [Freesurfer] General questions about freesurfer

Hi Scott, Thanks a lot... Kind regards, Arsene De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Scott Love Envoyé : mercredi 15 février 2017 11:19 À : Freesurfer support list

[Freesurfer] Q for posting on listserv

To FreeSurfer ListServ:  Dr. Iglesius recently responded to the questions below and asked that the question and response (also included below) be posted on the Freesurfer ListServ…Thanks very much. Questions on 13 Feb 2017: In the manuscript Iglesius et al, “A computational atlas of the

Re: [Freesurfer] tractstats2table error

Hi, could not be the issue python version mismatch? tractstats2table is python script, maybe there is a problem. Antonin Hi Adarsh – What operating system are you running this on? It runs fine for me with this input file when I test it on both a mac and a linux computer.a.y From:

[Freesurfer] Stats per region to brain map

Hi! I've been reading up on tkviewer etc. but can't figure out how to accomplish the following: I calculated some stats (outside Freesurfer) summarizing the relation between cortical thickness and my outcome measure, per region present in the Killiany/Desikan atlas (i.e. running analyses on data

Re: [Freesurfer] General question about freesurfer

Hi Arsene, Freesurfer tools have been adapted to work with species other than humans (e.g., dogs http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052140 ) but you cannot simply run the Freesurfer

[Freesurfer] DTI images, mri_glmfit-sim

Hello! I'm toying with some images acquired by following the dt_recon tutorial (fa-tal). I have prepared them for group analysis and run mri_glmfit, and the results look decent. However, I wanted to correct for multiple comparisons using for example mri_glmfit-sim --sim mc-full 100 2 cdbasename

[Freesurfer] General question about freesurfer

Hi everyone, I am a newbie in freesurfer. I went a little bit throughout the tutorials and few questions arose: 1) Is freesurfer was only built to process data acquired on primates (especially humans)? In other words, is freesurfer unable to process data from other animal models (rat, mouse,