Re: [Freesurfer] Manual correction for brainstem module

Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume e

[Freesurfer] Manual segmentation issues

Dear freesurfer users community, I need your help concerning manual segmentation issues. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is i

Re: [Freesurfer] Manual segmentation issues

Dear freesurfer users, I need your help concerning manual segmentation issues. In fact I used the editing tool with an intensity of 250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface. Some of th

Re: [Freesurfer] Manual segmentation issues

Hi Saturne you need to give us more information if you want us to help you. cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurfer users community,     I need your help concerning manual segmentation issues. ___ Freesurfer mail

Re: [Freesurfer] Manual segmentation issues

Hi Antoine if you upload the entire subject dir we will take a look. It sounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not. cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurf

Re: [Freesurfer] mri_glmfit-sim error

This is the command line output for mri_glmfit: [adits123@localhost projectoutputdata]$ mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd

Re: [Freesurfer] Cortical Thickness of a Volume-defined ROI

Dear freeSurfer, Thank you. I can use mris_anatomical_stats for the labels that are already defined, but when I want to define a new label, it does not work. My first problem is that when I define a new label on fsaverage, it does not save it for me and it gives me the following error: mghRead(/

[Freesurfer] Freesurfer for other species

Hi all, I was wondering if anybody else is using Freesurfer on non-human subjects? Thank you, Daiana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

[Freesurfer] cerebellar surface

Hi all, Freesurfer generates a volumetric parcellation of the cerebellum, but is there a method to generate the surface reconstruction, or perhaps just a hull surface from freesurfer output. Jim The materials in this email are private and may contain Protected Health Information. If you are

Re: [Freesurfer] Freesurfer for other species

I am, sort of. Feel free to email me directly with questions. stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699 On Mon, May 9, 2016 at 11:09 AM, Daya P wrote: > Hi all, > > I was wondering if anybody else is using Fr

Re: [Freesurfer] Manual segmentation issues

​ sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3... ​Dear Bruce, Most of the time the added voxels are included in the orig file but are lost in the ?h.white one. Here is the subject file. Thanks a

Re: [Freesurfer] Manual segmentation issues

Hi Antoine we need the entire subject directory tarred and gzipped if you want us to look. And please upload it to our ftp site thanks Bruce On Mon, 9 May 2016, Saturne Fox wrote: ​[icon_10_generic_list.png]   sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png] ​Dear Bruce,   

Re: [Freesurfer] Confirming the FC steps

Hi Dr. Greve, Thanks for all your help. After displaying second level functional connectivity maps (actually when I display subject-wise FC maps also), I tried to match the seed region location on FC maps using tksurfer, I found that that at the seed-region partial correlation coefficient (pcc) va

Re: [Freesurfer] Free surfer Gray Matter

Hi Gaurang we don't edit the gray matter/pial surface directly. We usually edit the white matter or change intensity thresholds in the mris_make_surfaces call to improve the accuracy of the pial surface. You need to figure out why it is not accurate (is the white surface accurate? Is the aseg

Re: [Freesurfer] Customized ColorLUT - opacity value that will make regions totally transparent?

Hi Stephanie, I think you will need to use the dev version of Freeview for the "alpha" value to work properly. hth d On Thu, May 5, 2016 at 12:08 PM, DeCross, Stephanie N. wrote: > Hi all, > > I’m trying to open a couple aseg.mgz labels and color code them. I thought > I’d do this by making my

[Freesurfer] LME parpool matlabpool update

Hey, Not sure if this could save someone else the trouble. The LME fitting software wasn't working for me since I updated Matlab, which has now switched from matlabpool to parpool for parallel processing, so I switched the call in the scripts to parpool, which seems to be working fine. Please fin

Re: [Freesurfer] LME parpool matlabpool update

Hi Sean, thanks for sharing. Our dev version already has an update for parpool (falling back to matlabpool to support older matlab versions). Also some code to detect the parallel toolbox and run single thread when it is not available. We merged those updates back via a pull request into Jorge

[Freesurfer] Pediatric longitudinal processing

I'm looking to use FS for longitudinal processing in a pediatric population ranging from 6-18 years. From what I've read, the longitudinal stream isn't appropriate because our data violate the assumption of fixed head size. Any advice on how to account for increases in head size would be appreci

Re: [Freesurfer] Pediatric longitudinal processing

Hi Zoe, there are basically two approaches if the assumption of fixed head size is violated: - use the longitudinal stream and see how far it get's you. Especially if the time delta is relatively small, this has good chances to work. It may require edits, so definitely check the results carefu

Re: [Freesurfer] Correcting defect

Hi Bruce, I already double checked and it looks like all time points are from the same subject. Please find attached the processing commands I used step-by-step (the same I sent you in the previous mail about this question). Do you need some more detailed information? Cheers. Katarina Katarin

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alp

[Freesurfer] Cluster Color

Free Surfer Support, I have been using the command line version for group analysis since my data set has too many factors for QDEC. There are a few things that I enjoy about QDEC that I wish I could incorporate into the command line. 1) In QDEC the cluster color is not set arbitrarily, but rathe

Re: [Freesurfer] Confirming the FC steps

no, that is not normal, you must have done something wrong :( On 05/09/2016 12:09 PM, Martin Juneja wrote: > Hi Dr. Greve, > > Thanks for all your help. > After displaying second level functional connectivity maps (actually > when I display subject-wise FC maps also), I tried to match the seed >

Re: [Freesurfer] mri_glmfit-sim error

It looks like over half your voxels have been pruned because they have value identical to 0 in at least one subject Found 149926 points in label. Pruning voxels by thr: 0.00 Found 65950 voxels in mask How did you create rh.paired-diff.thickness.sm05.mgh? On 05/09/2016 10:24 AM, Govindaraj

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

On 05/09/2016 04:11 PM, Ajay Kurani wrote: > Hi Doug, >Thanks for the explanation. In using p=0.05 with my thickness files > (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ > cdf file. > > In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean > the ov

Re: [Freesurfer] cerebellar surface

Hi Jim, You can use mri_tessellate. Regards, Thomas On Mon, May 9, 2016 at 11:11 PM, Alexopoulos, Dimitrios < alexopoulo...@kids.wustl.edu> wrote: > Hi all, > > > > Freesurfer generates a volumetric parcellation of the cerebellum, but is > there a method to generate the surface reconstruction,

Re: [Freesurfer] GLM - covariate question

Pedro, Instead of saying that you want to include the covariate in the analysis, it's better to consider why you want to include the covariate and how it changes the interpretation. You don't necessarily want to regress out covariates, especially when the covariate is different between groups. DO

Re: [Freesurfer] mri_glmfit-sim error

First did the mris_preproc and then the mri_surf2surf. Followed the group analysis wiki basically. Thanks Koushik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.e

Re: [Freesurfer] mri_glmfit-sim error

how did you compute the difference? Can you send the mris_preproc and mri_surf2surf command lines? On 5/9/16 10:26 PM, Govindarajan, Koushik Athreya wrote: > First did the mris_preproc and then the mri_surf2surf. Followed the group > analysis wiki basically. > > Thanks > Koushik > >

[Freesurfer] Big ventricles and recon-all error

Dear FreeSurfer group, I am having problems with a subject with very large ventricles. The recon-all exits with errors. Is it known issue that FreeSurfer is having difficulties with large ventricles? How can i solve this problem? I have read in another post, that the flag -bigventricles may sol

[Freesurfer] 3T flag

Dear FreeSurfer group, Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment. However, where can i find the documentation for the abo