Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Dear Mark, Just to make sure we’re on the same page: I’ll say that two images are in the same voxel space when they have the same size (in voxels, e.g., 256x256x256) and the same vox2ras matrix - the one that maps voxel coordinates to RAS (physical)

Re: [Freesurfer] kvlGEMSMatlab error: search direction is not a descent direction

External Email - Use Caution Dear Wayne, We have an idea of what the problem might be and will look into it soon. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs

[Freesurfer] -cw256 flag in recon-all

External Email - Use Caution Hello FreeSufer developers, We're trying to have a small quality control pipeline when executing recon-all. As a part of this, one doubt came to us, and couldn't find an answer: Is the -cw256 flag applied always or only when the FOV is larger than

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

External Email - Use Caution Dear Douglas, thanks a lot. This can solve my problem. Could you please give my some explanations about how to open and use the tool? Thanks Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Ph

Re: [Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information

External Email - Use Caution Dear Doug, Thank you for your help. On the query on atlas, We have a atlas that was built at our institute comprising of 183 regions and these 183 regions are available each as a nifti file with the probability information of finding the structure a

[Freesurfer] Complete CSF value computation

External Email - Use Caution Hi Team, We would like to compute the CSF value from the MRI data. We have both T1 and T2 weighted images. Have processed the T1 images and obtained the CSF value(summation of ventricular system and CSF value). But it

[Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hi Team, I have one doubt. Can I input T2 weighted images for recon-all command? Regards, Janani ::DISCLAIMER:: --

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

External Email - Use Caution Hi list, I'm running the follow command lines: 1) mri_glmfit --y ces.nii.gz --cortex --surf fsaverage rh --glmdir MMSE.wls --nii.gz --fsgd g1v1_MMSE.fsgd dods --C intercept.mtx --C slope.mtx --eres-save 2) mri_glmfit-sim --glmdir MMSE.wls --perm 100

Re: [Freesurfer] freesurfer masks for fsl processed data

Just run recon-all on the mni brain On 05/02/2018 07:12 PM, Rongxiang Tang wrote: > > Dear All, > > I ran fsl feat on my functional data and have all my data transformed > into standard MNI space. However, I would like to use freesurfer > generated white matter parcellation (wmparc.mgz) to extr

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

Please include previous emails so that I know what you are asking about. I get a lot of emails:) On 05/03/2018 05:07 AM, Lucia Billeci wrote: > > > Dear Douglas, > > thanks a lot. This can solve my problem. Could you please give my some > explanations about how to open and use the tool? > > Tha

Re: [Freesurfer] T2 weighted images as input for recon-all command

No, not currently On 05/03/2018 11:26 AM, M Janani wrote: > > Hi Team, > >    I have one doubt. Can I input T2 weighted images for > recon-all command? > > Regards, > > Janani > > ::DISCLAIMER:: > ---

Re: [Freesurfer] kvlGEMSMatlab error: search direction is not a descent direction

External Email - Use Caution Great! I am looking forward to your solution. Thank you, Eugenio. Best, Wayne On Thu, May 3, 2018 at 12:51 AM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > External Email - Use Caution > > Dear Wayne, > > We have an idea of wha

[Freesurfer] transforming functional volumes to MNI without resampling

External Email - Use Caution Hi, I'm trying to register and transform some raw functional data (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low res dimensions. I have tried: bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold mri_vol2v

[Freesurfer] V6 Stable OSX software error - multistrip flag

External Email - Use Caution I'm using the following flags on my recon -all: -mprage -time -multistrip -subcortseg and getting the following errors at this section of the log file: mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_a

Re: [Freesurfer] Trouble getting git-annex files

Hello Ruy, The -r flag to will cause the build to skip some dependencies, e.g., sometimes makefiles will rebuild the world when you don’t need them to, so if you are building only 1 file, then it can be useful. It works for me to cd to ./freesurfer/trc and do the same thing without using -r, i

Re: [Freesurfer] transforming functional volumes to MNI without resampling

What is funcVol? An individual functional? If so, then use --12 (12 dof to account for scaling). In general, we don't recommend doing cross subject registration with BBR as it is really not appropriate for that kind of thing. On 05/03/2018 01:30 PM, David Beeler wrote: > > > Hi, > > I'm trying

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Yes, we are on the same page, thank you so much for the advice. One followup question - is the threshold on the binary masks 50%? Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPh

Re: [Freesurfer] Trouble getting git-annex files

External Email - Use Caution Thank you for your help Rob. Could you walk me through how you ran setup_configure and configure on Mac? I ran (from the root of the tree): ./setup_configure ./configure F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 CXX=/usr/local/bin/g++

Re: [Freesurfer] combinesurfs problem: shifts and rotates

Try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_convert On 05/03/2018 03:05 AM, Klink-3, N.E.C. van wrote: > External Email - Use Caution > > Unfortunately no, same shift and rotation. > And in addition messed up vertices... > > > Nicole > > -Oorspronkelijk ber

[Freesurfer] (Follow-Up) Interaction Contrast

External Email - Use Caution Dear Douglas, Thank you for your guidance. I am following-up on your response with regards to setting up DODS matrix to test interaction between two continous covariates. If I understand your recommendation correctly (please correct me if I am wrong

Re: [Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all

External Email - Use Caution Hello, In the past we have only used the T1 image as input for recon-all. However, we are now also acquiring a FLAIR image and were thinking of using both for new studies. Does anyone have any data on the differences/advantages of using FLAIR images

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Sorry I have a few questions. The original images were NOT 256x256x256, they were cropped, but it seems that all of the output images from Freesurfer are 256x256x256. The simplest thing for me to do is to register my DTI images to the nor

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Hi Mark, Even if the freesurfer recon-all stream images are 256^3, they are still in the same physical RAS space as the input. No need to worry about that. I don’t know how FSLview handles orientation / RAS coordinates; I encourage you to use FreeSurf

Re: [Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all

No data, but people generally say that it improves the pial placement in terms of avoiding dura On 05/03/2018 03:46 PM, O'Shea,Andrew wrote: > > > Hello, In the past we have only used the T1 image as input for > recon-all. However, we are now also acquiring a FLAIR image and were > thinking of

Re: [Freesurfer] mri_segment-MRIcheckVolDims error

Hi Kambiz we need more information than this to help you. Can you send us the full recon-all command you ran and the recon-all.log? cheers Bruce On Thu, 3 May 2018, Kambiz Tavabi wrote: External Email - Use Caution Hi all, I noticed the following error message in a reconal

Re: [Freesurfer] Trouble getting git-annex files

Hello Ruy - sending you a followup off list to your email. - rob On May 3, 2018, at 3:16 PM, Ricardo Valle mailto:ruyval...@gmail.com>> wrote: External Email - Use Caution Thank you for your help Rob. Could you walk me through how you ran setup_configure and configure on Mac? I ran

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hi Freesurfer developers, I have executed the recon-all command using the T1 images but I would be interested in doing a reconstruction of the hippocampal subregions using for that purpose a higher resolution images (eg T2 or FLAIR) as input. I read he

Re: [Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi Bruce, I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surf

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Yes, we are on the same page, thank you so much for the advice. One followup question - is the threshold on the binary masks 50%? Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPh

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Hi again, You pick the most probable label at each voxel. In a binary segmentation problem, that amounts to thresholding at 50%. By with more labels, it does not, eg if p(a)=p.4, p(b)=0.3 and p(c)=0.3, you pick a even though p(a)<0.5. Cheers E Sent f