Re: [Freesurfer] Improve normalization with own average subject

Hello, I have computed the lh.sphere.myreg3 and rh.sphere.myreg3 files for all of my subjects as outlined on the web page on this topic (chapter: Creating a registration template from scratch). Now I would like to know which points in those registered files correspond to each other. How do I ha

Re: [Freesurfer] Brainmask edit error

Hi Sabrina, Could you upload the whole subject folder to the FTP or to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ I can play around with the data a bit to see if we can improve surfaces. If that doesn't work then we can discuss other options for how to get the information you ne

[Freesurfer] Tract length

Hi Imagers - I am looking at the Uncinate fasciculus in a Cannabis use disorder (CUD). I found that CUD subjects have significantly shorter tract length and a significant group x side interaction in comparison with controls. Have you seen this before? What is the interpretation of this finding?

Re: [Freesurfer] Tract length

Hello, I wouldn't mind jumping on this issue more broadly. Diffusion indices like FA, ADC, RD, and AD have more clear physiologic correlates. But what does the length of a tract, the volume of a tract, or the number of streamlines say about physiology? Tract length seems to be very dependent

[Freesurfer] FreeSurfer 5.3 OASIS

Hello, I've been trying to process a subject from the OASIS database with FreeSurfer 5.3. FS is relative new to me. I'm trying to use recon-all with -all but the format img/hdr does not seem supported. Do you have any ideia what should I do to process these images? Thank you. Sincerely, Vitor __

Re: [Freesurfer] White matter segmentation

I added --2009s to my command (mri_vol2vol) but it didn't give me the white matter labels yet. I used following code can you tell me how should I modify it? /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon1 /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon2 /usr/local/freesurfe

[Freesurfer] recon-all on 0.5mm scan?

Hi Freesurfer I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to

Re: [Freesurfer] FreeSurfer 5.3 OASIS

HI Vitor can you send us your command line and full screen output? We definitely support img/hdr, but note that it may not contain enough info to figure out the true anatomical directions (e.g. left from right) cheers Bruce On Wed, 25 May 2016, Gouveia, Vítor wrote: Hello, I've been tryin

Re: [Freesurfer] DTI error

Hi Anastasia, I am still receiving the following error message when I run a different participant doing, trac-all -path –c dmrirc1_sim.txt: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt If you have any ideas for what i can try it would be very appreciated! Thanks! Jasmin On Sun, Ma

Re: [Freesurfer] DTI error

Good call! Thanks Anastasia! It worked! On Wed, May 25, 2016 at 8:46 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Jasmin - On my screen the dash "-" symbol before the "c" looks > different than the one before "path". I'd check if you are indeed typing a > plain "-c". > > Be

Re: [Freesurfer] DTI error

Hi Jasmin - On my screen the dash "-" symbol before the "c" looks different than the one before "path". I'd check if you are indeed typing a plain "-c". Best, a.y On Wed, 25 May 2016, Jasmin Alves wrote: Hi Anastasia,  I am still receiving the following error message when I run a different

Re: [Freesurfer] FreeSurfer 5.3 OASIS

Dear Bruce, Thank you for your reply. I think I've just discovered the issue. I was using Ubuntu 16.04 and it seems that FS does not work with Ubuntu 16.04. I've just tried with Ubuntu 14.04 and FS is working. I'm now processing one image. The commands that I use: recon-all -subjid fsresult -i O

Re: [Freesurfer] errors in wm and pial boundaries

Hi Bruce, just checking in to see if you have had an opportunity to take a look at the data I sent over? Thanks Corinna On Wed, May 18, 2016 at 6:19 PM, Corinna Bauer wrote: > Sure. I'm uploading now. The above is approximately slice 75, although the > control points/wm surface problem is seen

Re: [Freesurfer] Tract length

Hi Anthony - Thanks for your input. You have raised very important points. I looked at the literature and found a paper where they look at FBL - fiber bundle length. Lauren E. Salminen ,[image: corresponding author] Peter R. Schofi

Re: [Freesurfer] White matter segmentation

That link says to use mri_aparc2aseg, not mri_vol2vol On 05/25/2016 11:21 AM, Mahmoudi, Fariborz wrote: > I added --2009s to my command (mri_vol2vol) but it didn't give me the white > matter labels yet. I used following code can you tell me how should I modify > it? > > /usr/local/freesurfer/bin

Re: [Freesurfer] Need Help

recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm tksurfer yoursubjectname lh pial -ov $SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3 On 05/24/2016 08:34 PM, HARI GURAGAIN wrote: > Hello, > > I am kind of new to the neuroimaging. I was trying to reproduce the > following

Re: [Freesurfer] Need Help

Thanks a lot. It helped. > On May 25, 2016, at 3:24 PM, Douglas N Greve > wrote: > > recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm > tksurfer yoursubjectname lh pial -ov > $SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3 > > > On 05/24/2016 08:34 PM, HARI GURAGAIN wr

[Freesurfer] surfaces from 0.5mm scan

Hi there My initial email didn't seem to have sent and so I am re-sending it: I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if th

Re: [Freesurfer] surfaces from 0.5mm scan

Hi Trisanna you can use the -cm flag, but typically what we do is let recon-all "conform" the data to 1mm, then do a post-hoc surface deformation with the original highres data using mris_make_surfaces cheers Bruce On Wed, 25 May 2016, Trisanna Sprung-Much wrote: > Hi there > > My initial ema

Re: [Freesurfer] surfaces from 0.5mm scan

thanks Dr. Fischl, Would there be a reason as to why recon-all crashed when doing the conformation then? I got the following error in my terminal: Original Data has (0.5, 0.5, 0.5) mm size and (394, 466, 378) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data

[Freesurfer] request for corrected p-values for mni305 space

Hi, just a user request for corrected p-values for the mni305 space analyses (i.e., sig.voxel.nii.gz files). Thanks! Joe Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Mar

[Freesurfer] New to Freesurfer; cortical thickness

Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other m