Re: [Freesurfer] How FDR was used to correct for multiple comparisons

Dear Douglas, Thank you for your reply. I run “mri_fdr –help” to get docs that include some information for how to use this command. However, I still don’t know how FDR was used to correct for multiple comparisons. This question is an opinion given by one reviewer, and I really don’t know how t

Re: [Freesurfer] problem with mri_label2vol for aseg

Hi Bruce, If I *just run the mri_convert command that you provided, it did not work. The result is the same, with randomly labeled voxels along the boundaries of GM. *Am I supposed to run mri_convert and then also run the mri_vol2vol command? I don't understand what you mean by trilinear sampl

Re: [Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

I probably shouldn’t say this too loud but, after many delays, I might be close to having a working atlas of the thalamic nuclei that I would like to release in FreeSurfer. Hopefully in a couple of months… -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University

[Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

Hi all, Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools? Or somehow transform the ROI from an atlas into subject space, then extract volume data? Thanks, Yash ___ Freesurfer mailing list Freesurf

[Freesurfer] Map the vertices that show a relationship between the FC (obtained by FS-FAST)

Hi there, I wonder if the fsgd file and the command lines listed below are corrected. My sample included 4 groups with different diagnosis (g1, g2, g3, g4). I'm interested to map the vertices that show a relationship between the FC (obtained by FS-FAST) and cortical thickeness, regressing out the

Re: [Freesurfer] FSGD design for multi-centre study

Hi, I just wanted to ask again regarding my question below. I've noticed that 2 of the centres contribute a smaller number of subjects and don't in fact have any female controls. Should I remove these as classes (ie. take out control_Female_centre1 and control_Female_centre2) and then change t

Re: [Freesurfer] How FDR was used to correct for multiple comparisons

You can also use mri_fdr Run  it with --help to get docs On 04/16/2018 10:23 AM, Livia Liu wrote: > > Dear FS experts, > > I'd like to know that how FDR was used to correct for multiple > comparisons. I do FDR correction in two way in FreeSurfer. > > 1, Do the FDR correction in the qdec tool. An

[Freesurfer] FSFAST, Beta values and Percent Signal Change questions

Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my contra

[Freesurfer] Non-rigid registration approaches

Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.ni

[Freesurfer] How FDR was used to correct for multiple comparisons

Dear FS experts, I'd like to know that how FDR was used to correct for multiple comparisons. I do FDR correction in two way in FreeSurfer. 1, Do the FDR correction in the qdec tool. And the page of “False Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec” was lost. 2, Use

Re: [Freesurfer] reruns recon-all -long after edits

Hi Martin, thank you so much for the quick and helpful reply! As I only edited the wm.mgz in the base, there was still some non-wm included there in the long and also some minor edits to the brainmask.mgz were necessary that I had probably overlooked in the cross. To run this command recon-all -

[Freesurfer] Brainhack Donosti 2018, San Sebastián, Spain

Registration is still open for Brain Hack Donosti, 2018 http://www.bcbl.eu/events/BrainhackDonostia2018/en/conference/ Registration deadline: April 25th, 2018 Project submission deadline: May 1st, 2018 Hacking multimodal neuroimaging techniques to explore brain function and structure Welcome to

Re: [Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

Douglas, I'm already extracting the data with mris_anatomical_stats -a SUBJ225/label/lh.lobesStrict.annot -b SUBJ225 lh But I would like to do it now for multiple subjects at once, as the data extraction. Righ now I'm just copying it to a table, one by one. Thank you! On Fri, Apr 13, 2018 at 8:1

Re: [Freesurfer] LGI for the lobar annotation

Thank you, Douglas, do you have any suggestions on how to make you work? Fernanda On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve wrote: > that should work, except the command line is not quite right > > On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote: > > Good night, > > does anyone kn

Re: [Freesurfer] Longitudinal processing with different FS versions

Thanks to both of you. On Mon, Apr 16, 2018 at 12:18 PM, Martin Reuter wrote: > Hi Susanna, > > yes, as you feared, you should rerun the first time point so that all time > points are run by the same version. Edits should be preserved (although > maybe more or probably less edits would be necess

Re: [Freesurfer] Longitudinal processing with different FS versions

Hi Susanna, yes, as you feared, you should rerun the first time point so that all time points are run by the same version. Edits should be preserved (although maybe more or probably less edits would be necessary). And it is really a bad idea to compare across groups where the groups where pr

Re: [Freesurfer] reruns recon-all -long after edits

Hi Anna, yes, long can still be edited, but usually this is not necessary. What kind of edits did you need to do in the long? You would need to call with the long flag, and passing the cross and base name. So just like the regular processing of the -long step, only replace -all with -autorecon

Re: [Freesurfer] Longitudinal Freesurfer Analysis

Hi Katie, yes, you should check the base (subject-template) if further editing is necessary there, so that surfaces look good on the base. Best, Martin > On 4. Apr 2018, at 15:54, Mckay, Katie Geraldine > wrote: > > Hi, > I have a question regarding the longitudinal processing stream in Free

Re: [Freesurfer] Longitudinal strean including more than an image per time point

Hi Maria, you can include all time points per subject in the longitudinal processing. For the statistics I would add a time-varying co-variate with the head coil type. Best, Martin > On 13. Mar 2018, at 11:45, Maria Paternina Die wrote: > > Dear all, > > We want to run the longitudinal FS p

Re: [Freesurfer] ASEG and APARCSTATS2TABLE on longitudinal data

Hi Lisa, 1. It all depends on what kind of analysis you want to do. You can run aparcstats2table without the long_stats_slopes. Then you will get an entry for each time point. If you run long_stats_slopes it will compute the within-subject difference first, put the result into each base dire

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Lea, sorry for the late reply, just in case this is still of interest: 1. It is possible to process all cross data with 5.3 and then base and long with 6.0. As long as you do the same for all subjects it should be fine, just don't mix across subjects. Also depending on the size if only half