Re: [Freesurfer] mkcontrast-sess error

External Email - Use Caution Thank you for your reply. I checked and matlab was in my path. Nevertheless, I finally found a solution myself that I am happy to share for future reference. 1. I ran the command "which matlab" to get the path to matlab 2. I ran the command "ex

Re: [Freesurfer] Account password on Virtualbox VDI

External Email - Use Caution Hello Chris, Sending the password to your account shortly. - R. On Sep 18, 2020, at 13:10, Mcnorgan, Christopher wrote:External Email - Use CautionHi,I have a couple students who are windows users who I am trai

Re: [Freesurfer] Make BEM with corrected brainmask

Try: mris_expand lh.brainmask.surf 3 inner_skull From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kadwani, Manorama Sent: Friday, September 18, 2020 6:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Make BEM with corrected brainmask I read that the option "-thickness" exp

Re: [Freesurfer] Make BEM with corrected brainmask

I read that the option "-thickness" expands the surface by a fraction of its thickness. https://miykael.github.io/nipype/interfaces/generated/interfaces.freesurfer/utils.html#mrisexpand How to expand by distance in mm? I want to expand using distance. But when I use the option "-distance" I get

Re: [Freesurfer] Cohen's D calculation and interpretation

No, not unless you have another data set or you split your data into two sets. Using one set, you get the clusters, then compute the D from the other data set. On 9/18/2020 3:16 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Thank you for clarifying this confusing situa

Re: [Freesurfer] --inittp 0 in mri_robust_template

Hi Marisa, usually a random time point is selected as an initial registration target. From there we map all images (including the initial target) to a common mid space and create the first template there, then we register to that template and iterate. This speeds things up, but is theoreticall

[Freesurfer] Autorecon after control points error

External Email - Use Caution Dear Freesurfer developers, After we run recon-all in a subject we noticed some mistakes, so we added manually some control points in a point set we named control.dat. Then we tried to run autorecon, with the command: recon-all -autorecon2-cp -autorec

Re: [Freesurfer] error message using mri_robust_template

Hi Marisa, the main goal of robust_template is to remove rigid motion between scans. So the first question is, do you really need (want) affine? The next question is, if this still occurs in FS 7.1.1 I remember dimly that I worked on this some years ago (basically allow a larger threshold, as

Re: [Freesurfer] Functional connectivity preprocessing and seed analysis

External Email - Use Caution Dear Douglas, I uploaded the file and the file name is wenzhen.tar.gz. the file has freesurfer_results and template.nii.gz. Thank you for looking into the problem. Please let me know if you need anything. Best, Wenzhen > On Sep 18, 2020, at 12

Re: [Freesurfer] Cohen's D calculation and interpretation

External Email - Use Caution Thank you for clarifying this confusing situation for me. I am attempting to compute Cohen's d values for regions found to be significant following Qdec group analysis using Monte Carlo simulation while controlling for multiple comparisons. I apologize

[Freesurfer] Account password on Virtualbox VDI

External Email - Use Caution Hi, I have a couple students who are windows users who I am training remotely. They’ll be using the VDI found at: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 I’ve never tried this and can give no guidance, as I have no Windows computers at my disp

Re: [Freesurfer] voxel to ras transform written by mri_convert -c

On 9/18/2020 12:12 PM, Billah, Tashrif wrote: Hi there, How is the rightmost column in `mri_convert -c` calculated? I have the following fslhd (relevant fields shown only) in a NIFTI image: ``` dim1            208 dim2            300 dim3            320 qto_xyz:1       0.799690    0.022176   

Re: [Freesurfer] Autorecon after control points error

Can you upload the subject? Follow the instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (

Re: [Freesurfer] Resting state fMRI preproc-sess registration error

External Email - Use Caution Dear Douglas, I could not locate the log file, so I re-ran it, then copied all outputs here below. bbregister --mov sess01/rest/template.nii.gz --bold --s bw083 --lta register.dof6.lta tmp ./tmp.bbregister.19439 Log file is register.dof6.dat.lo

Re: [Freesurfer] Fwd: non-white matter hypointensity

External Email - Use Caution Thank you so much for the response from both of you. I guess I should upload the T1 brain image in fsaverage to show the hypointensity spots? Best, Lihong On Fri, Sep 18, 2020 at 11:35 AM Douglas N. Greve wrote: > I think these usually show up

Re: [Freesurfer] Fwd: non-white matter hypointensity

Yes, they are typically in gray matter, although I’m not sure we see them very often (sometimes in the basal ganglia I think) From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of L Sent: Friday, September 18, 2020 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: non-

Re: [Freesurfer] Resting state fMRI preproc-sess registration error

Can you send the bbregister log file? On 9/18/2020 12:02 PM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear Douglas, > > tkregisterfv --mov sess01/rest/template.nii.gz --targ subject/mri/orig.mgz > --reg register.lta > > This is the command that I used to check registration.

[Freesurfer] voxel to ras transform written by mri_convert -c

Hi there, How is the rightmost column in `mri_convert -c` calculated? I have the following fslhd (relevant fields shown only) in a NIFTI image: ``` dim1208 dim2300 dim3320 qto_xyz:1 0.7996900.022176 0.001352-86.687996 qto_xyz:2 -0.021442

Re: [Freesurfer] Resting state fMRI preproc-sess registration error

External Email - Use Caution Dear Douglas, tkregisterfv --mov sess01/rest/template.nii.gz --targ subject/mri/orig.mgz --reg register.lta This is the command that I used to check registration. I also checked them by opening Freeview and manually open the template.nii.gz with re

Re: [Freesurfer] Fwd: non-white matter hypointensity

I think these usually show up in putamen/pallidum, in which case they are probably mineralization, a virchow-robin space, or maybe a subcortical stroke. On 9/18/2020 11:28 AM, L wrote: External Email - Use Caution Dear experts, I am wondering what the non-white matter hypointensity

Re: [Freesurfer] Converting Volume ROI to Surface .annot file

You can use mri_vol2surf to sample it on the surface, then use mris_seg2annot to create an annotation with it. BTW, you can probably just use the output of mri_vol2surf in your matlab program instead of the hassle of working with annotations On 9/16/2020 3:40 PM, Paul Dhami wrote: Ex

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output {Disarmed}

External Email - Use Caution Hi! Thanks, Doug and Bruce, for your input. It seems to be a problem with the number of iterations (-n). It is currently hard coded to run 4 times. If I run it only once, grey and white are in a normal range (but there are still inhomogeneities). If I r

Re: [Freesurfer] mkcontrast-sess error

It looks like matlab is not in your path. On 9/18/2020 5:55 AM, Bianca Sieveritz wrote: External Email - Use Caution Dear FreeSurfer Developers, I have preprocessed my functional data using the FsFast function preproc-sess and am now attempting to set up contrasts for first level an

[Freesurfer] Fwd: non-white matter hypointensity

External Email - Use Caution Dear experts, I am wondering what the non-white matter hypointensity refers to. Does it refer to hypointensity in subcortical regions or all brain regions except white matter? When we do data analysis using volume results from ROI tables, we found a

Re: [Freesurfer] mri_surf2surf template rh.white to fsaverage5

run mri_surf2surf  with --help and see example 3 On 9/16/2020 9:01 PM, 1248742467 wrote: External Email - Use Caution hello,Fs Because I want to build an N*N matrix based on the fixed-point number N of rh.white, but the original rh.white has too many fixed-point numbers, a memory er

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

It's been a while since 5.3, but I vaguely remember something like this happening because there were one or two super bright voxels in the image. If this is the case, then you can find them and clip them. On 9/18/20 10:32 AM, Fischl, Bruce wrote: I don’t think adding 100 will work as once it

Re: [Freesurfer] Recon-all crooked volumes

I don't think there is anything wrong with it. The subject just has his/her head tilted a fair amount in the scanner. The final analysis looks ok from here On 9/17/20 1:14 PM, Hasimoglu, Yasemin wrote: Hello, I recently ran recon-all on a group of subjects with FreeSurfer 7.1.0, and for one

Re: [Freesurfer] papers that have reported results using FS5.2

The issue was that some code was inserted into the surface deformation algorithm that helped the Wash U HCP images, but made the surfaces quite inaccurate on many other acquisitions. Are there actually papers that used it? I think we found the issue within a couple of weeks and retracted the ver

Re: [Freesurfer] Prescan normalize and freesurfer

#2 is the safest. I think #1 is probably ok, but you'll want to check that the 12% does not correlate with some factor of interest (eg, all 12% in the control group) On 9/17/20 8:12 AM, Mikolas, Pavol wrote: External Email - Use Caution Dear Freesurfer Developers, I am analyzing the

Re: [Freesurfer] left-right flip?

External Email - Use Caution Thanks for your reply Doug. Yes, I'm thankful I figured it out with your help! In the meantime I already tried to run mri_convert based on the mri_info --orientation information. For instance, if mri_info --orientation yielded "LAS" for the nifti,

Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

If you know the vertex number, then you can get the RAS in "tkregister space", eg, in freeview (other ways too),  then use #2 on that page On 9/17/20 4:18 AM, Fred Sampedro wrote: External Email - Use Caution Thank you very much Prof Greve! I'm almost done! Now, using mri_volcluster

Re: [Freesurfer] Make BEM with corrected brainmask

Try mris_expand On 9/16/20 10:24 PM, Kadwani, Manorama wrote: Thank you, I got a brain surface using the mri_binarize function. Is there a function for expanding the surface radially by a few millimeters? I want to create the inner skull surface as an expansion of the brain surface. Thanks,

Re: [Freesurfer] Cohen's D calculation and interpretation

You have created a circularity that is classic in neuroimaging (see Vul's paper on "VooDoo Correlations"). By using only voxels inside a cluster, you have selected voxels that are sure to show hi D values On 9/16/20 7:48 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Hi

Re: [Freesurfer] Resting state fMRI preproc-sess registration error

Can you send the commands you used to check the registration ? On 9/16/20 2:24 PM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear freesurfer developers, > > I am working on preprocessing resting state fMRI and used the following > command. > > $ preproc-sess -s sess01 -fsd r

Re: [Freesurfer] left-right flip?

I'm sorry to hear it, but at least you figured it out. You're best option is just to convert directly from the dicoms if you have them using mri_convert, dcmunpack, or just passing a dicom file directly to recon-all as input. If you don't have access to the dicoms, you can run mri_convert input

Re: [Freesurfer] papers that have reported results using FS5.2

I can't remember what the issues where, but I don't think they were all that bad, something with surface placement. Bruce might remember better than me On 9/15/20 7:22 PM, Paul wrote: External Email - Use Caution Dear Freesurfer Developers, With Freesurfer 5.2 being listed as depreca

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

I don’t think adding 100 will work as once it scales everything down that far you only have a couple of bits of representation in the conformed ( 1 byte/voxel) images. Maybe someone else can comment on fixing nu_correct? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwi

Re: [Freesurfer] Viewing labels in freeview

Hi Bronwyn, Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3. Best, Ruopeng On Sep 18, 2020, at 2:03 AM, Bronwyn Overs mailto:b.ov...@neura.edu.au>> wrote: External

[Freesurfer] mkcontrast-sess error

External Email - Use Caution Dear FreeSurfer Developers, I have preprocessed my functional data using the FsFast function preproc-sess and am now attempting to set up contrasts for first level analyses. I have been able to run mkanalysis-sess, but am receiving an error when I tr

[Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

External Email - Use Caution Hi! I am having some issue at the interface between mri_nu_correct.mni and mri_normalize, using v5.3. Specifically, the output when applying mri_nu_correct to a T1 is quite dark, with white matter in the range of 15. Contrast is ok. When I apply mri_nor