Re: [Freesurfer] Help with V6

Hi Noah, this error is pretty weird. Can you please send us the exact command you executed? Regarding the runtime: your 2014b runtime won't work. You need to follow the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral r

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

Basically, I try to create the .mgh files from sig.nii.gz and ces.nii.gz files needed for mri_segstats in ROI-analysis. I run already preprocessing and selxavg3-sess stats to produce the different stats files (sii/ces.nii.gz) The .mgh files show the correct anatomy-space dimension (mri_info: 1x

[Freesurfer] correction for field dishomogeneity

Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): "Authors used an old 3 T MRI without using the appropriate pipeline provided

Re: [Freesurfer] Reasons for problems with resampling issues

Dear Douglas thanks a lot for your advice. I tried it, but only one volume of the stack was read. I tried to use the --frame option, but it does not work. How can I force mri_segstats with the --frame option so that all 53 volumes of the stack are read? Thanks in advance Regards Jürgen Am 02

[Freesurfer] longitudinal analysis

Dear Freesurfer experts In the command "long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR", Do-avg will compute the temporal average. I do not quite understand

Re: [Freesurfer] correction for field dishomogeneity

Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). ch

Re: [Freesurfer] recon-all: Same MRI, different execution tame

There are known and justifiable reason for potential differences in iteration count and run time of the code, potentially related to, but not limited to, random seed and convergence. But the case you demonstrate below is a bit extreme. And past experience running that code makes me dubious of th

Re: [Freesurfer] unique label from volume / surface ROIs

Hi Martin at the end of recon-all we correct the volume-based segmentations with the surfaces, so the aparc*.mgz files should be pretty accurate cheers Bruce On Thu, 2 Jul 2015, Martin Hebart wrote: Hi Doug, Thanks a lot. But aren't the aparc.a2009s+aseg.mgz the volume-based ROIs and aren

Re: [Freesurfer] correction for field dishomogeneity

Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying "without using the appropriate pipeline provided by freesurfer"? Thanks BW C Il giorno 03/lug/2015 15:32, "Bruce Fischl" ha scritto: > Hi Clelia > > yes, we correct for field inhomogeneity. Presumably th

Re: [Freesurfer] correction for field dishomogeneity

not sure. Did you use recon-all? If so, then you did use "the appropriate pipeline provided by freesurfer" On Fri, 3 Jul 2015, clelia pellicano wrote: > > Hi Bruce, > > thank you for your reply. Do you have any idea about what they could mean > saying "without using the appropriate pipeline pro

Re: [Freesurfer] how to make ROI using surface

Hi Bruce, Can you tell me how I can use mis_compute_layer_fractions ? I found it in dev_binary in http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/ . Thanks! Yun > On Jul 2,

Re: [Freesurfer] correction for field dishomogeneity

I did it. Thank you very much. C Il giorno 03/lug/2015 18:51, "Bruce Fischl" ha scritto: > not sure. Did you use recon-all? If so, then you did use > "the appropriate pipeline provided by freesurfer" > On Fri, 3 Jul > 2015, clelia pellicano wrote: > > > > > Hi Bruce, > > > > thank you for your r

[Freesurfer] tutorial materials

Hi, freesurfer experts: I am a newer to study freesurfer. I have completed recon-all for individual analysis. Next I want to study group analysis. I noticed there is a "qdec" folder under "group_analysis_tutorial", I go into "qdec" folder and check the content of qdec.table.dat with cat command. I

[Freesurfer] What algorithm does mri_label2label use?

Hi! We are using mri_label2label to map functionally defined ROIs from one anatomy to another (within subjects), using --regmethod surface. We were wondering which algorithm mri_label2label uses to map the labels? Is it using mri_surf2surf, and if so, which mapmethodis it using? Thanks, Caspar