Re: [Freesurfer] Fdr correction using command line

Thanks, Doug for the binary. A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa. If for example, I am

Re: [Freesurfer] how to exact the result of the stats filedir

We use mris_anatomical_stats. Is that what you mean? On 10/08/2016 05:33 AM, zhang yue wrote: > > Hello FreeSurfer Developers, > > I’m attempting to exact the result of ‘stats’filedir, such as file > ‘lh.aparc.stats’, I want to know you guys how to do this work. Your > kind reply would be

Re: [Freesurfer] Using caudate as a seed

11 and 50 11 Left-Caudate122 186 220 0 50 Right-Caudate 122 186 220 0 On 10/11/2016 10:56 AM, Raney, Talia L. wrote: > Hi, > Is there any way in FSFAST to use caudate as a seed for connectivity > analysis? I was checking to see if it

Re: [Freesurfer] Gamma / Histogram

On 10/08/2016 02:43 AM, Anders Hougaard wrote: > Dear Freesurfers, > > Please see the attached image. > It shows inflated fsaverage surface with gamma.mgh overlaid. > Gamma.mgh is from one contrast of a standard group analysis of > cortical thickness (two groups A and B, two contrasts A>B and

Re: [Freesurfer] smoothing kernel inconsistency

On 10/10/2016 08:20 AM, Qi Ting wrote: > Dear Freesurfer experts, > > I am trying to do the group analysis, before this I tried to smooth the data > with the different smoothing kernel. However, when I checked the output dir, > it turned out that data were smoothed with a larger smoothing

Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

If all you want to do is fdr correction you can use this program: https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr On 10/10/2016 07:31 PM, Mishra, Virendra wrote: > > Hi, FreeSurfer Users. > > I am comparing cortical thickness of 2 groups controlled for certain > variables of no

Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

Thank you, Doug. Regards Virendra -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 12, 2016 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] Remapping Volume

Try adding --projfrac 0.5 On 10/12/2016 11:29 AM, Crawford, Anna wrote: > I did: > > mri_vol2surf --src > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz > --out > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMnnS.mgh >

[Freesurfer] Checking Longitudinal Runs

Hello Experts, I have a question regarding the outputs to the longitudinal processing stream. I ran my two participant's scans through the Cross, then created a Base and two longitudinal runs. I am primarily interested in looking at ventricular change over time. Other than the aseg output

[Freesurfer] Error long_mris_slopes

Dear FreeSurfers, I've been trying to run a longitudinal cortical thickness analysis in FreeSurfer but unfortunately, so far, it has not worked. After preprocessing the data following the instructions from the tutorial, I tried running: *long_mris_slopes --qdec

Re: [Freesurfer] Remapping Volume

I used: --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh --regheader segfs --hemi lh --surf white --out_type mgh >From the help file online, it

[Freesurfer] Hippocampal subfield analysis in FS 6.0

Hello, I am about to start my project on hippocampal subfield analysis and realise that this function is highly improved in FS version 6.0. I have run my data in FS 5.3 before this came to my knowledge, and I am now wondering when version 6.0 will be released to the public so I can run them

Re: [Freesurfer] Hippocampal subfield analysis in FS 6.0

Dear Synne, There will hopefully be a beta release of 6.0 some time soon, but it’s hard to tell exactly when (please see recent messages on the list by Bruce Fischl and Zeke Kaufman about this topic). Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group

Re: [Freesurfer] [Dev Build] Processing very high resolution dataset

Dear all, using mris_topo_fixer instead of mris_fix_topology also results in a segmentation fault. The command line used was: mris_topo_fixer -mgz -warning -seed 1234 lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /surf/lh.orig... Before

Re: [Freesurfer] Issues processing brain hemispherectomized patients

Hi Hinke mri_em_register, mri_ca_label, mri_ca_register and mri_ca_normalize all take -lh and -rh commands to indicate that only one hemisphere exists. Try including them and see if it fixes things (you should be able to use expert options for this). We have only used it for ex vivo analysis

Re: [Freesurfer] Segmentation editing

if the surfaces are fine probably not, but you will want to recreate the stats tables cheers Bruce On Tue, 11 Oct 2016, firet...@web.de wrote: Dear experts   after editing aseg the Segmentations wiki says one: " could recreate the final surfaces with the command: recon-all

Re: [Freesurfer] Quantifying volumes

Dear Doug, Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray

Re: [Freesurfer] Hippocampal subfield analysis in FS 6.0

Hi Synne we are (hopefully!) in the final stages of alpha testing and will release a beta soon cheers Bruce On Wed, 12 Oct 2016, Synne Aanes wrote: Hello, I am about to start my project on hippocampal subfield analysis and realise that this function is highly improved in FS version

Re: [Freesurfer] Remapping Volume

that seems ok, as I think the default is nearest neighbor. Can you visualize the volume you created and see if the incorrect labels are in it? On Wed, 12 Oct 2016, Crawford, Anna wrote: > I used: > > --src >

Re: [Freesurfer] [Dev Build] Processing very high resolution dataset

Hi Falk you are almost certainly running into a problem with some MAX number of defects/faces or something. If you upload the subject dir I'll fix it cheers Bruce On Wed, 12 Oct 2016, Falk Lüsebrink wrote: Dear all,   using mris_topo_fixer instead of mris_fix_topology also results in a

[Freesurfer] Issues processing brain hemispherectomized patients

Dear all, I’m having troubles getting a good Freesurfer output from a hemispherectomised brain using recon-all. I was wondering whether there’s someone that has experience with running Freesurfer on such an unusual brain? The first couple of issues I bumped into were failures regarding the

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

The problem appears to be that the PET or the MRI (or both) have incorrect voxel sizes (about 15%). You need to fix the problem. You can get a decent registration using something like mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg dof9.wb.lta --dof 9 --no-ref-mask --ref

Re: [Freesurfer] Remapping Volume

That seems to have worked and the regions are solid now. Thank you! Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, October 12, 2016

Re: [Freesurfer] group analysis

Dear Douglas and Trisanna, Thank you very much for your explanations. I just would like to be sure of what I am doing since there is no example on the wiki as complex as mine. If I have the following classes : Diagnosis : Patient or Control Gender : Male or Female Site : Site1 or Site2 or

Re: [Freesurfer] question about Unpaired T-test group analysis

On 10/11/2016 11:41 AM, kinson li wrote: > /Hello, / > / > / > /Question 1: I would like to conduct an Unpaired T-test group > analysis, I have two group of people, Group A8 age is 8 and Group A9 > age is 9, and I to test the/ change in thickness with age. But I am > little confusion about

Re: [Freesurfer] Fdr correction using command line

The sign depends on how you set up the contrast. If you are using an FSGD file and have two classes A and B and a contrast [+1 -1], then positive indicates A>B. The F.mgh is the map of F values which are unsigned. The gamma.mgh file will have the contrast values themselves including sign. The

Re: [Freesurfer] Fdr correction using command line

Thank you for that clarification,Doug. VM On Oct 12, 2016 12:09 PM, "Douglas N Greve" wrote: > The sign depends on how you set up the contrast. If you are using an > FSGD file and have two classes A and B and a contrast [+1 -1], then > positive indicates A>B. The

[Freesurfer] Cortical Thickness Zero Values

Hello All, Quick question, I ran recon-all with the qcache option and after converting the ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am noticing some vertices have 0mm thickness and it varies, for example, one subject had 53 vertices labeled as zeros while another had over

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Thank you for your diagnosis Douglas. How could I get the voxel sizes right from input nifti pet and mri data ? Best regards, Matthieu Le 12 oct. 2016 10:05 PM, "Douglas N Greve" a écrit : > The problem appears to be that the PET or the MRI (or both) have > incorrect

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

you need to go back to the source data. At some point someone set or changed the voxel size to the wrong thing. This can sometimes happen in PET as reconstruction into volumes is not all that standardizeed On 10/12/2016 06:12 PM, Matthieu Vanhoutte wrote: > > Thank you for your diagnosis

[Freesurfer] Cortical Thickness Overlay Slice by Slice

Hello Freesurfer Experts, I am using Freeview to visualize cortical thickness with the command freeview -v mri/T1.mgz \ -f surf/lh.pial:overlay=lh.thickness While the cortical thickness overlay is visible in the 3-Dimensional display, I was wondering if it was possible to also view the cortical

Re: [Freesurfer] Cortical Thickness Overlay Slice by Slice

Hi Sancgeetha you can use mri_surf2vol to sample the thickness into the volume if you want. The thickness file itself does not contain any topological information - that is stored in the surface files (e.g. lh.pial) cheers Bruce On Wed, 12 Oct 2016, Sancgeetha Kulaseharan wrote: Hello

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

That is surface-based smoothing. the voxel size differences create differences in volume-based smoothing (a partial volume effect). I don't know of a good way to simulate volume-based PVC. This cannot be done in qdec On 10/06/2016 06:36 PM, Martin Juneja wrote: > Dear Dr. Greve, > > Thanks a

Re: [Freesurfer] mri_average vs mri_concat

Hmmm, I don't know what could be going on. Can you send the command line and all terminal output? On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote: > Hi Doug > > So the pixel values are 0 and 1 *in the original .mnc*. It seems that > after performing mri_vol2surf they become 0 and 255, and

Re: [Freesurfer] Fdr correction using command line

try this binary https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > Hi, > > I was wondering if there is a way to perform fdr correction using > command line in freesurfer without using matlab as mri_glmfit-sim only > does bonferroni

Re: [Freesurfer] Gamma / Histogram

Excellent, thanks! 2016-10-12 20:27 GMT+02:00 Douglas N Greve : > > > On 10/08/2016 02:43 AM, Anders Hougaard wrote: > > Dear Freesurfers, > > > > Please see the attached image. > > It shows inflated fsaverage surface with gamma.mgh overlaid. > > Gamma.mgh is from one