Re: [Freesurfer] segmentation help

In this regard I've decided to change the dataset. We're going for ADNI Dataset where I can find data in various format(nifti, mnc). Is there any other dataset I can find labeled dataset for Hippocampus segmentation. Thank you for helping me! Dilip On Mon, Apr 10,

Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

sorry, not easily. I guess you could recon them in the newer version then try using mri_label2label to transport them to the older one, but it isn't trivial since the fsaverage coordinate system has changed Bruce On Mon, 10 Apr 2017, Taylor, Johnmark wrote: (the reason I did this was

Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

(the reason I did this was because the new Freesurfer version outputs labels for perirhinal cortex as part of the reconstruction process, and we were interested in using this ROI in our analyses; as an additional question, is there a way of producing these anatomical labels without reconstructing

Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

Hi JohnMark lots of things change between versions and it is not possible to go back unless you just run the old version cheers Bruce On Mon, 10 Apr 2017, Taylor, Johnmark wrote: Hello, Recently, I re-ran recon-all with Freesurfer version 5 on some subjects whose surfaces had previously

[Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

Hello, Recently, I re-ran recon-all with Freesurfer version 5 on some subjects whose surfaces had previously been reconstructed with Freesurfer version 4. As a result, it appears that their surface reconstructions have subtly changed, such that the labels that were specified in the old

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

They are being run but do not need to be. It does not change the results, but it is not needed and wastes cycles. On 04/10/2017 04:24 PM, Antonin Skoch wrote: > Dear Doug, > > do you think that it is necessary/useful to rerun > > -normalization2 > -maskbfs > -segmentation > > steps after wm.mgz

Re: [Freesurfer] Surface down sample by taking cortical vertices only

Hi Dorothy, That would be extreme under sampling. I don't expect it to be very meaningful. hth d On Mon, Apr 10, 2017 at 2:42 PM, Dorothy Sincasto wrote: > Hi > > I want to do an MEG analysis and first I want to downsample the surface to > around 100 vertices per

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

oops, sorry, I thought you were asking about your other question... On 04/10/2017 04:45 PM, Douglas N Greve wrote: > I'm not sure. The problem is in the segmentation. There are several > steps in the segmentation, and it actually gets it right in the early > ones but then undoes it later on.

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

I'm not sure. The problem is in the segmentation. There are several steps in the segmentation, and it actually gets it right in the early ones but then undoes it later on. There are some parameters that can be played with (eg, -prior 0.5), I just have not had the chance to dig into it. On

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

Dear Doug, do you think that it is necessary/useful to rerun -normalization2 -maskbfs -segmentation steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell. In contrast, it seems to me that the

Re: [Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

I don't know if this is fixed or not, but you can use mri_vol2vol with the --regheader option and specify the interpolation method with --interp On 03/29/2017 06:25 PM, Harris Hoke wrote: > > I’m currently running freesurfer 6.0.0, and I’ve run into the same > problem described in this thread

Re: [Freesurfer] calculating geodesic distances between vertices

Mukund Balasubramanian did something with barycentric coordinates to solve this problem, but I don't know whether he ended up publishing it or not. On 03/30/2017 06:19 PM, Burke Rosen wrote: > I am interested in finding the distance between two vertices along the > cortical surface. > > So

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

It estimates the FWHM from the residuals of the analysis (it does not use whatever value you smoothed it with). For some reason this estimate is not-a-number (NaN). Are you using a mask? Can you send the terminal output from running mri_glmfit? On 03/31/2017 03:29 AM, Clara Kühn wrote: > ah,

Re: [Freesurfer] FreeSurfer : About ROI analysis

Yes, that is fine On 03/31/2017 05:42 AM, Lisa Delalande wrote: > Hello Doug, > > Yes this mail was quite difficult to write, so I resume : > First, I did a thickness analysis on Freesurfer > Then, with the clusters found, I draw ROIs and extracted the > statistical values (command : creation

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote: > Dear experts, > > I noticed inconsistency between recon-all -help and actual code of > recon-all in -autorecon2-wm option. > According to the recon-all --help the -autorecon2-wm processes

Re: [Freesurfer] correlation coefficient R

Try something like mri_segstats --i pcc.mgh --seg cluster.ocn.mgh --excludeid 0 --sum cluster.pcc.dat On 04/07/2017 08:35 PM, tom parker wrote: > Hi Doug, > > Thank you for your answer! > > It would be great if you could send me some instructions. > > Thanks for the help! > > Douglas N Greve

Re: [Freesurfer] create mask from cluster number?

mri_binarize --i HC.43.rh/v1.slope/results.ocn.mgh --match 1 --o cluster1mask.mgh You can concatenate all your subjects together in fsaverage space (mris_preprpoc), optionally smooth it, then mri_segstats ---i yourstackallsubjects.mgh --excludeid 0 --seg HC.43.rh/v1.slope/results.ocn.mgh

Re: [Freesurfer] Volume vs cortical thickness

The thickness is an average of two numbers. One is the distance from a white surface vertex to the pial surface along the normal to the white. The other is the distance from the pial to the white along the normal to the pial. Volume (in v6) is computed as the volume of a truncated tetrahedron.

Re: [Freesurfer] dimension mismatch between source and mask

You should only need those first two commands (+ the mri_mask). Use --interp nearest with the ribbon On 04/10/2017 12:27 PM, Maria Hakonen wrote: > > Hi Bruce, > > > Thank you for the reply! I have now tried: > > > mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh > --tal

Re: [Freesurfer] Ventricle-to-Brain Ratio

Doug, Thank you very much! That helps clear things up for me. Best, James On Mon, Apr 10, 2017 at 2:21 PM, Douglas N Greve wrote: > sorry, I would use these two > > TVV = left lateral ventricle + left inf lateral ventricle + right > lateral ventricle + right inf

Re: [Freesurfer] dimension mismatch between source and mask

Probably you'll want to use mri_vol2vol so that you can incorporate your registration between the fMRI and the anatomical On 04/10/2017 10:28 AM, Bruce Fischl wrote: > Hi Maria > > are they in register? If so you can do: > > mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz > mri_mask

Re: [Freesurfer] Ventricle-to-Brain Ratio

sorry, I would use these two TVV = left lateral ventricle + left inf lateral ventricle + right lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th ventricle + 5th ventricle + choroid plexus TBV = BrainSegVolNotVent On 04/10/2017 09:43 AM, Gullickson, James wrote: > Hi

[Freesurfer] Surface down sample by taking cortical vertices only

Hi I want to do an MEG analysis and first I want to downsample the surface to around 100 vertices per hemisphere. I tried the command mris_downsample, but when i plot the surface I see that the vertices go deep into the white matter. Is there an option to extract for example 100 equidistant

Re: [Freesurfer] dimension mismatch between source and mask

Hi Bruce, Thank you for the reply! I have now tried: mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh --tal --talres 2 mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal --talres 2 mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz mri_mask

[Freesurfer] Volume vs cortical thickness

Dear Freesurfer experts, I highly appreciate if anybody clarify how Freesurfer calculate cortical thickness and gray matter volume. If the cortical thickness of e.g. precentral gurus is measured as the closest distance from the gray-white boundary to the gray-CSF boundray at each vertex on the

Re: [Freesurfer] white matter edits not incorporated.

Dear All, I wanted to know if there is any take on the issue of white matter edits (specifically deleting unwanted voxels from wm.mgz). I sent a subject a week ago for your review. It seems this is a problem that I had with several scans, and by the message list, I am not the only one. Recent

Re: [Freesurfer] QDEC and ROI drawing

Sorry, I don't know what is going on with qdec. Why do you need to do this in qdec? If it is to draw labels, then you can also use tksurfer. On 04/10/2017 11:34 AM, Arnaud Boré wrote: > Hi Douglas, > What more can I do to help you figure out what's wrong ? > Thank you in advance > Arnaud > >

Re: [Freesurfer] TR: FreeSurfer : About ROI analysis

Yes you can do that correlation. Is that your only question? On 04/10/2017 09:59 AM, Lisa Delalande wrote: > Hello Doug, > > Yes this mail was quite difficult to write, so I resume : > First, I did a thickness analysis on Freesurfer > Then, with the clusters found, I draw ROIs and extracted the

Re: [Freesurfer] QDEC and ROI drawing

Hi Douglas, What more can I do to help you figure out what's wrong ? Thank you in advance Arnaud 2017-04-07 16:50 GMT-04:00 Arnaud Boré : > There is no shift in freeview. > > 2017-04-07 16:35 GMT-04:00 Douglas N Greve : > >> Not yet. Did you try

Re: [Freesurfer] dimension mismatch between source and mask

Hi Maria are they in register? If so you can do: mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz cheers Bruce On Mon, 10 Apr 2017, Maria Hakonen wrote: Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as

[Freesurfer] dimension mismatch between source and mask

Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz However, I am getting an error " dimension mismatch between source and mask". Could someone please let me know how to solve this problem? Best, Maria

[Freesurfer] TR: FreeSurfer : About ROI analysis

Hello Doug, Yes this mail was quite difficult to write, so I resume : First, I did a thickness analysis on Freesurfer Then, with the clusters found, I draw ROIs and extracted the statistical values (command : creation of .label and mris_anatomical_stats-l..label-t rh.thickness-b-f

Re: [Freesurfer] Ventricle-to-Brain Ratio

Hi Doug, To clarify: to calculate VBR, I need two things: a measure of TBV *and* and measure of TVV. I'm just wondering what the best way to derive each of these is. Thanks, James On Fri, Apr 7, 2017 at 11:24 AM, Douglas N Greve wrote: > I would use the TVV > > >

Re: [Freesurfer] segmentation help

you can also just give them to recon-all directly. Analyze is a dangerous format to use however as it doesn't allow you to determine left from right. Hopefully you have some type of fiducial marker in the image (e.g. a vitamin E tablet) cheers Bruce On Mon, 10 Apr 2017, Nina Jacobsen wrote:

Re: [Freesurfer] segmentation help

Hi Dilip you should go through our online tutorials. They explain all of this in detail. cheers Bruce On Mon, 10 Apr 2017, Dilip Puri wrote: > Hi, > > To-do "recon-all" where should I keep all the files. I mean in which > directory. What are the command lines? > > > Hope for response. > >

Re: [Freesurfer] segmentation help

Hi Dilip, Try the mri_convert function to convert your images, so recon-all can read them: https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html Fra: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af

Re: [Freesurfer] segmentation help

Hi all, Actually I've images in Analyze7.5 format(.img/.hdr). Can anyone help me to reconstruct('recon-all') for this format. Thanks Dilip On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen wrote: > Hi Dilip. > > You have to place your files where the subject-directory

Re: [Freesurfer] segmentation help

Hi Dilip. You have to place your files where the subject-directory points. If you dont change the directory yourself, this is under freesurfer/subjects. For more info about recon all, see https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all