Re: [Freesurfer] Freeview in FreeSurfer 6.0

I think this may have been fixed in the dev build. Would it possible for you to try the dev build? You can download it here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev > On Aug 21, 2017, at 1:34 AM, Wu Jianxiao (Jadecci)

[Freesurfer] Labels from Pial surface

Hello FreeSurfer developers, Is it possible to have the segmentation labels after the pial surface is done in FreeSurfer? I mean once you do the topology correction and expand the inner cortical boundary to make the pial surface ; is it possible to have the inner and outer cortical boundaries as la

[Freesurfer] Problem opening freeview

Hello, I am having a problem opening up freeview in MobaXterm (a bash terminal) on my windows 7 machine. Although freesurfer is working, when I attempt to open freeview, it tells me that "XWin_Moba.exe has stopped working." Have you ever come across this issue? Thanks

[Freesurfer] mri_coreg

Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g. mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline). mri

Re: [Freesurfer] smoothing

Dear Dr Greve, Thank you so much for the detailed explanation. I have additional question and I highly appreciate any clarification. By reviewing the log file "mri_gtmpvc.log" I see that this program apply smoothing FWHM=6 mm on the input SUVR maps and the output mgx images are smoothed accordi

Re: [Freesurfer] mri_mcsim error

There is a bug when it tries to read the -mask command line arg. I've fixed it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_mcsim you can also just put --mask mask.mgh at the end of the cmd line On 08/19/2017 12:16 AM, Zhiliang Long wrote: > Dear FS experts: >I am writtin

Re: [Freesurfer] Labels from Pial surface

when you run mri_annotation2label you can specify the surface (--surface). By default, it uses white, but you can specify pial instead On 08/21/2017 11:33 AM, Fereshte wrote: > Hello FreeSurfer developers, > Is it possible to have the segmentation labels after the pial surface > is done in Fre

Re: [Freesurfer] mri_coreg

I don't think that is turned on by default. There is smoothing of the NMI historgrams, but that is unrelated On 08/21/2017 12:07 PM, John Anderson wrote: > Dear Dr Greve, > Kindly, I wanted to know why "mri_coreg" apples smoothing during > registration. e.g. > > mri_coreg --s subject --mov temp

Re: [Freesurfer] smoothing

It does not apply any smoothing. It attempts to remove smoothing, but you have to tell it how much smoothing to remove. You probably told it 6mm On 08/21/2017 12:15 PM, John Anderson wrote: > > Dear Dr Greve, > > Thank you so much for the detailed explanation. I have additional > question and I

Re: [Freesurfer] Cortical gyrification findings

It will all come down to whether the reviewers let you include non-sig results On 08/18/2017 04:37 PM, Martin Juneja wrote: > Hello FS experts, > > I am correlating some of the behavioral measures with cortical > thickness (CT) and cortical gyrification (CG) measures. > > - For CT-behavioral: I

Re: [Freesurfer] mri_glmfit-sim annotations

it just uses the annotation of the vertex with the maximum value. You can have it use the centroid by adding --centroid On 08/18/2017 07:33 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > I was wondering how the annotations for the clusters that came out of > mri_glmfit are picked

Re: [Freesurfer] Resample to cropped FOV in anatomical space

This might be easier to do with lta files, eg, when you run tkregister specify --ltaout file.lta. Once you have both LTAs, You can then use mri_concatenate_lta to multiply them together, eg mri_concatenate_lta file1.lta file2.lta output.lta output = file2matrix*file1matrix mri_concatenate_lta

Re: [Freesurfer] extract average thickness using label for every subject

The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple comparisons correction, so they are gennerated from all the input On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote: > OK, this works now, when I map

Re: [Freesurfer] mris_anatomical_stats output

We do not output xls. You will have to convert it manually On 08/18/2017 08:38 PM, std...@virgilio.it wrote: > Hi list, > how can I save the outputs of mris_anatomical_stats in xls file? > Thanks > Stefano > > > ___ > Freesurfer mailing list > Freesurfe

Re: [Freesurfer] asegstats2table output meaning

do you mean these? https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats On 08/18/2017 01:54 PM, Yizhi Lin wrote: > No in the directory you did asegstats to table > > On Fri, Aug 18, 2017 at 10:54 AM, miracle ozzoude > mailto:miracoo...@gmail.com>> wrote: > > Hello Yizhi, > > Thank

Re: [Freesurfer] asegstats2table output meaning

Hello Doug,  Yes. Thank you.  Best,  PAUL Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Monday, August 21, 2017 4:09 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] asegstats2table output meaning do you me

Re: [Freesurfer] Labels from Pial surface

And what labels does this mri_annotation2label give? Does it give the outer cortical boundary as well? On Tue, Aug 22, 2017 at 12:19 AM Douglas N Greve wrote: > when you run mri_annotation2label you can specify the surface > (--surface). By default, it uses white, but you can specify pial instea

Re: [Freesurfer] smoothing

Perfect! Please how can I choose the correct value for PSF in the manual psf is the scanner psf FWHM in mm were can I find this value? It does not apply any smoothing. It attempts to remove smoothing, but you have to tell it how much smoothing to remove. You probably told it 6mm On 08/21/2017 1

Re: [Freesurfer] Labels from Pial surface

whatever annotation you give it (eg, aparc). There are not separate labels for the inner and the outer. The distinction is in the xyz coordinates. If you don't give it a surface, it will use the xyz coords from the inner (white) surface. If you give it --surface pial, it will use the xyz coord

Re: [Freesurfer] smoothing

read the petsurfer page for how to select the psf On 08/21/2017 04:52 PM, John Anderson wrote: > > Perfect! > > Please how can I choose the correct value for PSF > in the manual psf is the scanner psf FWHM in mm were can I find this > value? > > It does not apply any smoothing. It attempts to re

Re: [Freesurfer] smoothing

It is not clear in the manual where can I find it. In pet surfer page "--psf FWHM is the full-width/half-max of the the point-spread function of the scanner as measured in image space. Eg, an HR+ is typically about 6mm." Is it in the DICOMs? Is there an y formula to calculate it? Any reference t

Re: [Freesurfer] extract average thickness using label for every subject

I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain the average value of each subject in each cluster. Are we writing about the same file? 2017-08-21 22:07 GMT+02:00 Douglas N Greve : > The numbers in that file are just indices indicating the cluster number > (eg, 1=cluster1, 2=cl

Re: [Freesurfer] smoothing

The PSF is not necessarily a known value. Usually people get the value from a phantom study done on the type of scanner they are using. You can look through the lit to see if someone using your scanner (and pet recon) has done this. On 08/21/2017 05:05 PM, John Anderson wrote: > > It is not cl

Re: [Freesurfer] extract average thickness using label for every subject

oh, sorry, i thought it was another file. yes, in the .dat file, the value is the mean from inside the cluster. The input is the file you passed with --y. from the help: csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a sub

Re: [Freesurfer] extract average thickness using label for every subject

OK, thank you. I appreciate your help. Patricia 2017-08-21 23:13 GMT+02:00 Douglas N Greve : > oh, sorry, i thought it was another file. yes, in the .dat file, the > value is the mean from inside the cluster. The input is the file you > passed with --y. from the help: > > > csdbase.y.ocn.dat - t

Re: [Freesurfer] Mean diffusivity on cortex?

The data in gtm.nii.gz is in floating point. If you want to change the gtm.stats file, you'll have to rescale the input, eg, fscalc input.nii.gz mul 1000 -o input-time-1000.nii.gz On 08/15/2017 04:09 AM, Shane Schofield wrote: > Hello Dr Greve, > > I have ran the command and got the data from t