Re: [Freesurfer] Orientation by direction cosines

here's the code if it is any help: for (c = 0; c < 3; c++) ostr[c] = '\0'; for (c = 0; c < 3; c++) { sag = Mdc[0][c]; // LR axis cor = Mdc[1][c]; // PA axis ax = Mdc[2][c]; // IS axis // printf("c = %d, sag = %g, cor = %g, ax = %g\n",c,sag,cor,ax); if (fabs(sag) >

[Freesurfer] dispaly retinotopy result

External Email - Use Caution Hi, FS experts!I used a retinotopy paradigm with four stationary wedges located at the horizontal and vertical meridians. (checkerboard flickering at 8Hz, 4 conditions, 16 seconds each * 4 repetitions:1. upper half of the vertical

Re: [Freesurfer] Orientation by direction cosines

External Email - Use Caution Hi Bruce, Thanks for your response. It would be really helpful if you explain how does it interpret from matrix. Thanks, Ritesh Mahajan - Original Message - From: "Greve, Douglas N.,Ph.D." To: "freesurfer" Sent: Friday, January 25, 2019

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Ok hopefully, the text is visible now. bash-4.2$ mris_fwhm USAGE: mris_fwhm Smooths surface data and/or estimates FWHM --i input --subject subject (--s) --hemi hemi (--h), or --lh or --rh --surf surf --label labelfile --cortex :

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Sorry for the confusion. The Va doesn’t let us access our gmails so I’ll send an email with the text from my city mail email address. On Friday, January 25, 2019, Bruce Fischl wrote: > Hi Amrita > > please don't take an image of the text and send us

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Please find comments inline below. best, Matthieu > Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Dear

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Douglas, Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ? It depends. If you are

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

Hi Amrita please don't take an image of the text and send us that. Just copy and paste the text directly into the email. This is *much* more useful for us. cheers Bruce On Fri, 25 Jan 2019, Amrita Bedi wrote: External Email - Use Caution

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is not working? On 1/25/19 10:56 AM, Boris Rauchmann wrote: External Email - Use Caution Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Pasted the text in the email but not sure if you can view it On Friday, January 25, 2019, Amrita Bedi wrote: > > > On Friday, January 25, 2019, Amrita Bedi wrote: > >> >> >> Here you go. >> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < >>

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

I don't see anything. On 1/25/19 11:56 AM, Amrita Bedi wrote: External Email - Use Caution [X] Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Hi Amrita, can you just paste the text into the email? thanks doug On 1/25/19 10:51

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution On Friday, January 25, 2019, Amrita Bedi wrote: > > > Here you go. > On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Hi Amrita, can you just paste the text into the email? >> thanks >> doug >> >> On

Re: [Freesurfer] Orientation by direction cosines

mri_info will do it. If you just want the orientation string, you can add  --orientation. Or do you still want the interpretation of the matrix? On 1/25/19 10:10 AM, Bruce Fischl wrote: > Hi Ritesh > > I think that mri_info will try to figure this out and tell you (in the > "Orientation"

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. wrote: > Hi Amrita, can you just paste the text into the email? > thanks > doug > > On 1/25/19 10:51 AM, Amrita Bedi wrote: > > External Email - Use Caution > Hi Dr Greve, > >

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Good thing it's not the software :) Also makes it easier for me to fix. In my script there was one tiny mistake - the anatomical image for one subject was repeated each time instead of using the files for different subjects. I ran recon-all 100+ times

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

Hi Amrita, can you just paste the text into the email? thanks doug On 1/25/19 10:51 AM, Amrita Bedi wrote: External Email - Use Caution Hi Dr Greve, Ran mris_fwhm and got the attached. On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Based

Re: [Freesurfer] Surface to volume conversion

Hi Emma can you run mri_info on the .mgh and .nii.gz volumes and send us the output? Is the sig.mgh a surface overlay? If so, you can't visualize it directly, you have to overlay it on a surface (in either .mgh or .nii.gz foramt) cheers Bruce On Fri, 25 Jan 2019, Bunting, Emma wrote:

Re: [Freesurfer] FSFAST poor registration

Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files, but I'm relieved it was not my software:). On 1/25/19 5:09 AM, Keri Woods wrote: External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

I believe this python2 issue has been fixed in the dev version found here https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mris_slopes best, Andrew On 1/25/19, 10:08 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi Falk

[Freesurfer] cortical thickness calculation based on hammersmith segmentation

External Email - Use Caution <>Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all

[Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Hi Dr Greve, Ran mris_fwhm and got the attached. On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Based on the output below, it looks like there are problems with running > one of the freesurfer binaries. Can

Re: [Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello Bruce, Doug and Emanuel, I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded the development version and tried that, but neither procedures fixed the problem. In the meantime, my father-in-law took a week and fixed the

Re: [Freesurfer] move statistical map onto the cerebellum surface

Hi John --projfrac assumes that we know the thickness at each point, which is probably not true in your case, unless you have models of the top and bottom of the cerebellar cortex. You can use projdist instead, which takes a distance in mm (0 would mean you are sampling at the gray/white

Re: [Freesurfer] Orientation by direction cosines

Hi Ritesh I think that mri_info will try to figure this out and tell you (in the "Orientation" output). cheers Bruce On Fri, 25 Jan 2019, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > Can any one please explain how we come to know whether it is RAI or RAS or

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

Hi Falk thanks for catching the typo. I fixed it - nice to have an easy thing to fix for a change :) Bruce On Fri, 25 Jan 2019, falk.luesebr...@med.ovgu.de wrote: External Email - Use Caution Dear Juergen,   Thanks for your quick reply! Actually the spelling error is

Re: [Freesurfer] mri_convert

Hi Nazain I can't replicate this problem. Can you verify that the aseg.mgz is correct? If it is, maybe email me those 3 files as well as the complete output of mri_convert? cheers Bruce On Fri, 25 Jan 2019, N Saf wrote: External Email - Use Caution Dear Bruce, I had a

Re: [Freesurfer] How to extract cortical features of a ROI

Hi Kan if you draw a volumetric label you first need to sample it to the surface of that subject (mri_label2label --sample). If all you want are stats from the subject there is no need to map it to fsaverage - that is only necessary if you want to use a group coordinate system. cheers Bruce

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Dear Douglas, Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ? 2) Is this rescaling applied before PVE correction or after (i.e.

[Freesurfer] Vertex-wise area anlaysis

External Email - Use Caution Dear Freesurfer Experts, First of all: Thank you so much for your work and your fantastic product. I turn to you with a short question, I hope it is not too unnecessary and can be answered quickly. My interest lies in vertex wise longitudinal

Re: [Freesurfer] move statistical map onto the cerebellum surface

External Email - Use Caution Hi Dr Greve, yes indeed I used the flag "projfrac" and I missed including it in my command bellow. I greatly apologize! My I kindly ask, if "projfrac" is not used then at which layer of the cerebellum the projection will take place, is it 0.5?

[Freesurfer] Neuroscientist with focus on electrophysiology and imaging in Parkinson disease patients!

External Email - Use Caution *Doctoral Student* *Neuroscientist with focus on electrophysiology and imaging in Parkinson disease patients * The *clinic of neurology, imaging and neurostimulation group (http://imaging-neurostim.com ) University of

[Freesurfer] Orientation by direction cosines

External Email - Use Caution Hello Team, Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines: Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear all, I am getting the same problem on ubunto 18.04 without WSL. I would be glad for advice how to fix it. Best, Lars Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution I was able to circumvent the error by switching from python3 to python2. In python3 print was changed to a function making it necessary to put the arguments in brackets. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear Juergen, Thanks for your quick reply! Actually the spelling error is in the error message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes # extensive error checks #if options.fsgd is None and if options.qdec is None: #

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear Falk I have no idea, but recognised that the error refers to --qedc and not to --qdec. maybe there is a spelling error somewhere that is related to your problem. HTH Cheers Jürgen

[Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline successfully using the WSL? I'm running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I'm trying to process my first longitudinal data set following the

[Freesurfer] mri_convert

External Email - Use Caution Dear Bruce, I had a problem with bringing aseg.mgz into my subject space and you recommend this command before: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz which perfectly worked for me but now when I want to try it in new