Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Hi Matthieu I think 6.0 looks better overall, even in the beta that you have. The 5.3 segmentation looks like it is underestimating cerebellum and hippocampus to me. cheers Bruce On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote: > Dear FS's experts, > > I have tried the recon-all process on

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

1) what partial volume correction do you mean? 2) I'll leave this for Eugenio and Koen. Bruce On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, All right then it's only a question of time ofr the new v6 release ! Meanwhile, is it possible and coherent : 1) to use the partial volume

[Freesurfer] Fw: Gray matter intensity

Hi, Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans? Thank you very much.

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Hi Matthiew we are still hoping to get an official v6 release out in the next month or two, so it would be best to use that which I think will outperform whatever beta you have and 5.3. If you can't wait you are probably better off using 5.3 (although I think the v6 you have is more

Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote: > > Hi, > > > Just following up on my previous email (see below) as I have not yet > heard back. I also have another question regarding the lh.wm.mgh and > rh.wm.mgh generated by pctsurfcon. How do I view these as surface > overlays on T1 brain scans?

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

It is not subsegmented in 6.0 either:). When you run gtmseg, it will create the new segmentation that include pons and a few other things On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote: > Dear Douglas, > > Please see below : > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

btw, we are still making changes to version 6 so don't assume that the results from the beta will be consistent with the current beta distribution. On 12/15/2015 12:22 PM, Bruce Fischl wrote: > Hi Matthiew > > we are still hoping to get an official v6 release out in the next > month or two, so

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

It seems problematic to me to use a nightly dev build for publication. cheers, -MH --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [Freesurfer] R: Re: recon-all base error

Hi Salvatore, can you send - the FS version you are using - the recon-all command you called - the recon-all.log file thanks, Martin On 12/15/2015 02:00 PM, salvatoreandrea...@libero.it wrote: I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I

[Freesurfer] PALS B12

I am trying to a brodmann mask using PALS B12 atlas in fsaverage. I used the following command to create the volume from annotation file. I have two questions associated with it. mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o PALS_B12_Brodmann_Mask.nii --annot-table

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Not necessarily. It needs a good segmentation, so, to the extent that v6 has a better segmentation then v6 is better. On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote: > > Thanks Douglas for the answer ! > > But isn't PVC design for better working in terms of results with > v6_beta than v5.3 ?

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote: > Dear experts, > > Could anyone answer to my questions below ? > > Thanks ! > > Best regards, > Matthieu > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte > >: > > Dear FS

Re: [Freesurfer] Tracula Processing Question

Hi Doug - Yes, this is possible and indeed it is recommended to use the latest version of tracula. Best, a.y On Fri, 6 Nov 2015, Douglas Merkitch wrote: Hello FreeSurfer experts, We have a large dataset that was processed in FreeSurfer v 5.1 and we would like to run tracula on the

Re: [Freesurfer] Tracula with multi-shell data?

Hi Henrik - There's no explicit parameter in the current version, but you can run bedpostx the multi-exponential model yourself, and then let tracula use the orientation estimates from that model (as long as the output dir is called dmri.bedpostX, it'll read the files from there). We are in

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Hi Bruce, All right then it's only a question of time ofr the new v6 release ! Meanwhile, is it possible and coherent : 1) to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ? 2) to use

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

I mean that they may/will change between the current beta release and the final release. On 12/15/2015 02:51 PM, Matthieu Vanhoutte wrote: > > Sorry Douglas I didn't well understand what you mean. Did you mean > that results from beta distribution aren't valuable ? > > Best regards, > >

Re: [Freesurfer] Tracula_weighted dti metrics values

Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats).

[Freesurfer] Viewing more than one label at once in Freeview?

Hi, I am trying to show 3 aparc labels on the inflated surface, each in a different color, let’s say lh.inferiortemporal, lh.middletemporal and lh.superiortemporal . I have 2 questions: First I ran mris_annotation2label to extract the individual region aparc labels. I can merge them into a

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Dear Douglas, Please see below : 2015-12-15 18:37 GMT+01:00 Douglas N Greve : > > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote: > > Dear experts, > > > > Could anyone answer to my questions below ? > > > > Thanks ! > > > > Best regards, > > Matthieu > > > >

Re: [Freesurfer] Question about running recon-all with deface

Hi Bruce, When the thickness/volume measure was compared between the results obtained with recon-all with and without defaced T1 as input to recon-all, we obtained 20% errors (between them) Example: 100*(Thalamus_left_volume_with_defaced_T1_to_recon-all MINUS

Re: [Freesurfer] Tracula stats COR-.info does not exist

Hi Simon - You are correct, this was a bug specific only to running the -stat part of trac-all with the CVS template. Your work-around was correct. I've fixed the bug so that, as of the next version, the configuration as shown in the sample config file should work with the -stat part as

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

me too On Tue, 15 Dec 2015, Harms, Michael wrote: It seems problematic to me to use a nightly dev build for publication. cheers, -MH --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington

Re: [Freesurfer] Question about running recon-all with deface

I see. That is surprisingly large for whole structure volumes. We don't have a lot of experience analyzing defaced volumes, so I would do recon-all on the original data, then deface post-hoc. If you upload one subject where you find a large (or the largest) difference, I'll take alook On

Re: [Freesurfer] ERROR: Could not create directory

Hi Ju - Are you using the same computer and are logged in in as the same user when you create the directory manually and when you run trac-all? It's hard to replicate this error. What the program does at that point is run the system call mkdir -p

Re: [Freesurfer] TRACULA NaN values in stats files and empty stats file

Hi Deniz - It sounds like the reconstruction for this particular tract and subject may have failed. You can try reinitializing it by using the reinit variable in your configuration file (search reinit in the freesurfer email list archives for previous posts on this). If you try that and the

Re: [Freesurfer] dmri_motion tracula timepoint to timepoint motion, or timepoint to reference?

Hi Ruth - It expects the output format of eddy_correct. It then computes the transforms between consecutive frames from the transforms between each frame and the reference frame. Best, a.y On Sun, 29 Nov 2015, Ruth Carper wrote: Hi,  I'm hoping to use the dmri_motion tool to quantify

Re: [Freesurfer] TRACULA preprocessing error

Hi Doug - This post from the archives addresses the same error message. Please check if this fixes it for you, too: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37920.html Best, a.y On Mon, 9 Nov 2015, Douglas Merkitch wrote: Hey D, I also had the same error in the same

Re: [Freesurfer] Tracula - configuration file error

Hi Laura - It appears that you're using a different configuration file than the one you attached. To use Laura.txt, you should pass it as the argument to the "-c" option (instead of /scratch/lm618/tutorial_data/diffusion_tutorial). Best, a.y On Sun, 8 Nov 2015, L. Moreno-Lopez wrote: > Dear

Re: [Freesurfer] TRACULA visualisation differences

Hi Amanda - These are probability distributions, so this has to do with how you threshold them. When you use the -tv option in freeview to open the merged file with all tracts, each of them is thresholded at 20% of its maximum. When you open one of them as a plain volume, freeview doesn't do

Re: [Freesurfer] TRACULA question- pathstats not loading

Hi Noa - If you're still having this issue, please send the complete trac-all.log file and your configuration file. It's impossible to guess what goes wrong without seeing the full output. Best, a.y On Fri, 30 Oct 2015, Golan, Noa wrote: > Hi, > I am currently analyzing DTI data and I am

Re: [Freesurfer] Tracula Tracts density

Hi John - This is a probabilistic tractography method, so it draws samples from the probability distribution of the particular tract, and then adds up these sample streamlines to estimate the probability distribution. The number that you see is the number of sample streamlines. It's a

Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Sorry Douglas I didn't well understand what you mean. Did you mean that results from beta distribution aren't valuable ? Best regards, Matthieu Le 15 déc. 2015 19:24, "Douglas N Greve" a écrit : > btw, we are still making changes to version 6 so don't assume that the

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Thanks Douglas for the answer ! But isn't PVC design for better working in terms of results with v6_beta than v5.3 ? Best regards, Matthieu Le 15 déc. 2015 19:02, "Douglas N Greve" a écrit : > It is not subsegmented in 6.0 either:). When you run gtmseg, it will >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Dear experts, Could anyone answer to my questions below ? Thanks ! Best regards, Matthieu 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte : > Dear FS experts, > > 1) First Is it possible to use the partial volume correction provided in > the v6 beta version of

Re: [Freesurfer] recon-all base error

Hi - how much memory do you have on your machine? On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea...@libero.it < salvatoreandrea...@libero.it> wrote: > Hi Freesurfer experts! > > I tried to run recon-all base for a longitudinal analysis on my data. But > I get the following error: > > > >

[Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Dear FS's experts, I have tried the recon-all process on one subject with both FS v5.3 and v6_beta. Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other structures as cerebellum, hippocampus, ... I will attached in the FileDrop

[Freesurfer] Problem with mri_surf2surf inside mris_preproc

Hello - I am having a similar error to this post from 2011: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019290.html ...but as far as I can tell, no answer was given to this post. Perhaps I am just not seeing it? I am taking some contrasts that I computed in volume space for

Re: [Freesurfer] Problem with mri_surf2surf inside mris_preproc

Your surfaces are out-of-synch. This is usually caused by recon-all crashing or only running autorecon2 but not autorecon3 On 12/15/2015 05:31 PM, Ed Vessel wrote: > Hello - > > I am having a similar error to this post from 2011: >

Re: [Freesurfer] PALS B12

On 12/15/2015 03:19 PM, Woo, Jonghye wrote: > I am trying to a brodmann mask using PALS B12 atlas in fsaverage. I used the > following command to create the volume from annotation file. I have two > questions associated with it. > mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o >

[Freesurfer] Get summary stats for ROI

Hi Freesurfer Mailing List, I have just completed a GLM analysis with monte carlo correction and now have my "cache.th13.abs.sig.cluster.mgh" files showing the significant clusters for a specific contrast. I would now like to get mean cortical thickness values for these ROIs in another

Re: [Freesurfer] Get summary stats for ROI

Follow the same procedures that you used to get the input (--y) to mri_glmfit, then run mri_segstats --seg cache.th13.abs.sig.cluster.mgh --i y.new.mgh --excludeid 0 --avgwf avg.thickness.dat The avg.thickness.dat will be a file with a row for each subject and a column for each cluster doug

Re: [Freesurfer] PALS B12

Dear Doug, I’ve got the table from this command: mis_info lh.PALS_B12_Brodmann.annot & mis_info rh.PALS_B12_Brodmann.annot (https://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12) Thanks, Jonghye On Dec 15, 2015, at 6:23 PM, Douglas N Greve