Re: [Freesurfer] mri_vol2surf

External Email - Use Caution I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5 Now I'm just getting the error "freadFloat: fread failed" a whole bunch of times and the terminal gets stuck. Any suggestions? I checked

Re: [Freesurfer] mri_vol2surf

Specify a file format for the output (eg, C01.mgz) On 4/24/18 3:17 PM, Abdullah Ishaque wrote: External Email - Use Caution Hi, Thank you for the prompt response. I used the following command: mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the

Re: [Freesurfer] mri_vol2surf

External Email - Use Caution Hi, Thank you for the prompt response. I used the following command: mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5 This created two files called

Re: [Freesurfer] Segmentation issue with FS6

Hi Cody yes, it could be due to poor contrast. The watershed isn't the issue though, it is mri_segment and mris_make_surfaces. You can try changing the wm/gm limits, or upload the subject and we will take a look cheers Bruce On Tue, 24 Apr 2018, Barlow, Cody wrote: External Email

Re: [Freesurfer] Calculation of surface area

External Email - Use Caution Hi Douglas, Thanks for you answer. We actually tried this, but it gives other numbers, and the difference between the original surface area values and the ones we got through dividing was not consistent across regions Could there be another way?

[Freesurfer] Segmentation issue with FS6

External Email - Use Caution Hi FreeSurfer Experts, After running my subject through FS6 autorecon3 and QCing the data, I noticed that FS6 is outlining white matter as grey matter and then bumping out the grey matter segmentation accordingly. I have tried using different

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

Try permutation http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 4/24/18 8:21 AM, std...@virgilio.it wrote: Hi, I'm performing a group analysis. I would like to investigate a simple correlation analysis within group, aiming to map the clusters showing

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Thank you for the reply! I deleted the contrasts and run this command line: selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok --- matlab output MATLAB is selecting SOFTWARE OPENGL rendering.

Re: [Freesurfer] mri_vol2surf

That all looks correct. For the registration, just use --regheader C01 On 4/24/18 11:12 AM, Abdullah Ishaque wrote: Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart

Re: [Freesurfer] freesurfer selxavg3-sess error

Try deleting the contrasts (.mat files) and rerunning On 4/24/18 5:48 AM, Francesca Strappini wrote: Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

sorry, did not get it. Can you resend? On 4/23/18 8:25 PM, Ryan Flores wrote: > External Email - Use Caution > > Hi Doug, > > I just wanted to follow up on this. Were you able to download the zip file ok? > > Best, > > Ryan > > On 4/18/18, 10:46 AM, "Ryan Flores"

Re: [Freesurfer] resting state motion censoring

I think that will work On 4/23/18 3:08 PM, Adam Martersteck wrote: Hi Freesurfer team & Doug, Thought I would check in again about censoring volumes and using fcseedcor. I was thinking about if it hasn't been incorporated yet -- could I create my own first level covariate .dat file and

Re: [Freesurfer] Non-rigid registration approaches

Sorry, I don' know what to tell you. On 4/21/18 5:34 PM, Hedyeh Javaheri wrote: Thanks for your reply Douglas, I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion

Re: [Freesurfer] QDEC vs. Command Line Stream

They both give the same results for the same analysis. It is harder to do proper correction for multiple comparisons in QDEC On 4/20/18 12:50 PM, Arsenije Subotic wrote: Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to

Re: [Freesurfer] Calculation of surface area

you can try dividing it. Run this on subjects for whom you do have area and see how well it does On 4/20/18 8:15 AM, Zohar Berman wrote: Dear Douglas, Thank you for your quick answer! The thing is, we don't have access to the original surface area files which were created by FreeSurfer

Re: [Freesurfer] FSGD design for multi-centre study

Just remove the class. ps. Please remember to include previous correspondences so we have context On 4/20/18 6:19 AM, C.P.E. Rollins wrote: > External Email - Use Caution > > Thanks a lot for the explanation. The issue is that I don't think > Freesurfer will run a design for which

[Freesurfer] mri_convert

External Email - Use Caution Hello, I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker

[Freesurfer] mri_vol2surf

External Email - Use Caution Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject,

[Freesurfer] mris_convert Segmentation fault.

External Email - Use Caution Hi, I am planning to convert an ASCII file to a gifti file using mris_convert. I am using FreeSurfer 5.3 on Linux 9 stretch. The ASCII file includes the vertex id , its MNI305 coordinates and p value. Vertex id is 0-based, from 0 to 20483. I used

Re: [Freesurfer] correcting deffect

that's a pretty large defect - about 15% of the size of a typical surface. The defect correction complexity is quadratic in the convex hull of the defect, so it can take a *long* time for big defects. Usually one this big means something went badly wrong - a bunch of skull attached, or

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

External Email - Use Caution Hi, I'm performing a group analysis. I would like to investigate a simple correlation analysis within group, aiming to map the clusters showing correlation between the FC and the neuropsychological test scores (e.g. MMSE). Overall, the NPS test

[Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess