Re: [Freesurfer] Direction of significant group comparison

External Email - Use Caution Hey Doug, thanks so much for your answer! Do you mean the "Max" column? This is the only one that changes signs in all my results. I used abs in the analyses. So if the order in my FSGD file is subjects of the groups ADHD, Comorbid and Typically

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Hi John, I know others (Satra?) might have more recent experience. I used to be able to get recon-all down to about 4 hours. OpenMP made the most difference but the GPU code always helped if you have it running. It really depends on whether you can get

[Freesurfer] Calculated thickness

External Email - Use Caution Dear FS?? I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no outp

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution The scripts I used to manage upload, execution, and download of thousands of freesurfer runs to a cluster are available at https://github.com/mfschmidt/freesurfer-management. Seeing what I did might save you some time over scripting this from scratch. F

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Thanks for these clarifications. I added some others questions inline below. Best, Matthieu > Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote: >> >> Extern

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Thanks for these clarifications. I added some others questions inline below. Best, Matthieu > Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote: >> >>Externa

[Freesurfer] (no subject)

External Email - Use Caution Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > External Email - Use Caution > > > > > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > free

[Freesurfer] When segmentation went perfect but some pial is remaining: looking for advice

External Email - Use Caution Dear Free Surfer team, I am checking my group of HCs. I have seen that GM and WM segmentation is nearly perfect (for now) but, there are some point in which I can see more pial, but pial has not been considered in the segmentation. I have the believe,

Re: [Freesurfer] Calculated thickness

Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: External Email - Use Caution Dear FS??   I now have two different surfaces, the two su

Re: [Freesurfer] When segmentation went perfect but some pial is remaining: looking for advice

Hi Rosalia it really depends on the case. Can you send some images to show what you mean? Bruce On Fri, 7 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Free Surfer team, I am checking my group of HCs. I have seen that GM and WM segmentation is n

[Freesurfer] ?????? Calculated thickness

External Email - Use Caution Dear Bruce, I want to implement ThicknessRepeatibility, but I can't get the output mgh file in the last step. What is the reason? http://ftp.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility yu'jun'jie --

[Freesurfer] ?????? Calculated thickness

External Email - Use Caution The problem is in the fourth step of ThicknessRepeatibility - mris_surface_stats -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; : Re: [Freesurfe

Re: [Freesurfer] When segmentation went perfect but some pial is remaining: looking for advice

External Email - Use Caution Hi Bruce, Thank you a lot for your answer. The data is being transferring now via FTP (I learned how to from the last time!!). Rosalia On Fri, Dec 7, 2018 at 6:01 PM Bruce Fischl wrote: > Hi Rosalia > > it really depends on the case. Can you send so

[Freesurfer] gray intensity

External Email - Use Caution Dear Bruce, I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yujunjie___ Freesurfer mailing list Fre

Re: [Freesurfer] ?????? Calculated thickness

Hi yujunjie in general if you want our help you have to give us more information. We need for example the full command line you ran and the full output of it (in text, not a screen shot!) cheers Bruce On Sat, 8 Dec 2018, 1013364183 wrote: External Email - Use Caution The p

[Freesurfer] mri_segstats - different results with --ctab

External Email - Use Caution Hi freesurfer experts, I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation volume (parc2502dwi.nii.gz) and the corresponding color table with: for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ #

[Freesurfer] Questions About Effect Sizes in Vertexwise GLM Anlaysis

External Email - Use Caution Hi Freesurfer Experts, I have two related questions about the measures of effect size that can be derived from a vertexwise GLM analyses conducted in Freesurfer: 1. What is the unit of effect size for the gamma.mgh file created by vertexwise GLM Analy

Re: [Freesurfer] fsaverage6 FS6

External Email - Use Caution Many thanks Doug, that worked! Now that I resampled my data I'm having the next issue: smoothing. I'm using mri_surf2surf specifying the same source and target subject (resampled to fsaverage6), but apparently to skip the registration I need to also

Re: [Freesurfer] gray intensity

I defer to Doug and David on this one On Sat, 8 Dec 2018, 1013364183 wrote: External Email - Use Caution Dear Bruce,  I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yuju

Re: [Freesurfer] fsaverage6 FS6

Hi Rachele what is your command line? The ?h.sphere.reg is in register with fsaverage, but it looks like your data has been mapped to the fsaverage6 subject (which has 40962), but you are specifying the individual subject surface. If that is the case, use the fsaverage6 surface instead cheers

Re: [Freesurfer] fsaverage6 FS6

External Email - Use Caution Thanks Bruce, this is my command line (note that because of a different organization of the data, the subject dir is /Data/48/ and the subject is MRI_sMRI_fs_reconall_fs_reconall_gcv6s): mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv

[Freesurfer] glm analysis

Dear Freesurfers, I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 2)short disease duration MS, 3)healthy controls) and 1 variable (age). According to the formula provided on freewiki: N classes (N of variables + 1), is this contrast matrix correct? 1 -1 0 0 0 0

[Freesurfer] Error in running make_average_subject

External Email - Use Caution Hello!, I am getting the following error using the command make_average_subject mri/norm.mgz: could not load norm volume from (null) I have found this page with a path for de issue https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/

Re: [Freesurfer] Error in running make_average_subject

Hi Emanuel you need to send us the full command you ran and output of it if you want us to be able to help you cheers Bruce On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: External Email - Use Caution Hello!, I am getting the following error using the command make_average_subje

Re: [Freesurfer] Extracting ROI from atlases

External Email - Use Caution I tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use? Thank you so much in advan

Re: [Freesurfer] Extracting ROI from atlases

Hi Da-yea what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just

Re: [Freesurfer] Extracting ROI from atlases

External Email - Use Caution Hi Bruce, We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use? Thank you, Da-Yea -Original Message- Fr

Re: [Freesurfer] Extracting ROI from atlases

yes, use the fsaverage annot file. That is essentially what you want cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: External Email - Use Caution Hi Bruce, We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particula

Re: [Freesurfer] Extracting ROI from atlases

External Email - Use Caution Could you please direct me on where I could find the fsaverage annot file for the Desikan atlas? Thank you, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of

Re: [Freesurfer] Extracting ROI from atlases

$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot On Fri, 7 Dec 2018, Song, Da-Yea wrote: External Email - Use Caution Could you please direct me on where I could find the fsaverage annot file for the Desikan atlas? Thank you, Da-Yea -Original Message- From: freesu

Re: [Freesurfer] Extracting ROI from atlases

External Email - Use Caution I really appreciate the quick reply back Bruce! I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/su

Re: [Freesurfer] Extracting ROI from atlases

the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: External Email - Use Caution I really appreciate the quick reply back Bruce! I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate an

[Freesurfer] fcseedcor output

External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seed

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, I come back on my previous question concerning survival bias in LME. Do you have an advice ? Best, Matthieu > Le 19 oct. 2018 à 16:30, Matthieu Vanhoutte a > écrit : > > Hi Martin, > > Do you mean that high attrition (less time points

[Freesurfer] extracting the version of FreeSurfer used to process some data

External Email - Use Caution Hi FreeSurfers, I'm working with some data that has been collected and processed with FreeSurfer over several years. Consequently, some individuals have been processed with different versions of FreeSurfer. Is there a file in an individual's subject

Re: [Freesurfer] fcseedcor output

hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-se

Re: [Freesurfer] extracting the version of FreeSurfer used to process some data

look at subject/scripts/build-stamp.txt On 12/7/18 5:09 PM, David Groppe wrote: External Email - Use Caution Hi FreeSurfers, I'm working with some data that has been collected and processed with FreeSurfer over several years. Consequently, some individuals have been processed with

Re: [Freesurfer] fcseedcor output

External Email - Use Caution > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fcseed-sess, I used fcseedcor. the command > th