[Freesurfer] recon-all: .md and .txt format

Hello FS experts, I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were al

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, groups should be 0 and 1, e.g. 0 for controls, 1 for disease. Order of groups does not matter (as long as both X and Y are ordered that way). You can do FDR or FDR2 on your final sig values. It is best to combine results from left and right hemisphere and do a single FDR2 correction

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, yes, 0 0 0 1 is the interaction (if longitudinal slopes = atrophy rates, differ across groups). When interpreting these, it makes sense to look at your model: Y_ij = b0 + b1 t_ij + b2 g_i + b3 t_ij g_i where t is time, g is group. For group=0 you have Y_ij = b0 + b1 t_ij so b0 is th

Re: [Freesurfer] LME correction in longitudinal analysis

Dear Martin, Thank you very much for your quick reply. I use voxel-wise mixed model analysis, and I see different design: lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex);Summary: Algorithm did not converge at 0 percent of the total number of locations. lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,

Re: [Freesurfer] recon-all -all error end abruptly

Hi Ramesh just the same one as before - you ran out of memory, likely because something else was running at the same time cheers Bruce On Tue, 6 Jun 2017, Ramesh Babu wrote: Dear Bruce, Today I ran the image processing on the same image which was stopped abruptly earlier. Now it is finish

Re: [Freesurfer] recon-all: .md and .txt format

Do you have read permission to that file? On 6/6/17 3:45 AM, 곽유나 wrote: Hello FS experts, I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the fol

[Freesurfer] How to do a regular GLM in 2 groups with 2 times

Dear FS Experts,I want to measure the thickness difference between two groups, control and experimental group. And every subject scaned twice.I look at the page: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessingand some reply in Mail-list.I looked one method: Subtract time2 to time

Re: [Freesurfer] recon-all -all error end abruptly

Dear Bruce, I am using 16 GB RAM. Should I increase RAM OR upgrade my graphic card? Thanks Ramesh On Tuesday, June 6, 2017, Bruce Fischl wrote: > Hi Ramesh > > just the same one as before - you ran out of memory, likely because > something else was running at the same time > > cheers > Bruce >

[Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis

Hello, I have ran my data through the default recon-all processing stream and am planning on analyzing ventricular volume and cortical thickness. I was wondering whether I need to use the Qdec to complete the ventricular volume and cortical thickness analysis, or can I export the data (txt files f

Re: [Freesurfer] computational neuroanatomy position (fwd)

FYI -- Forwarded message -- Date: Tue, 6 Jun 2017 18:33:39 + From: "Reiser, Michael" To: Bruce Fischl Subject: Re: computational neuroanatomy position https://www.janelia.org/lab/reiser-lab/positions The Reiser lab at the Janelia Research Campus seeks a creative scienti

[Freesurfer] TRACULA -path issue

Hi all, I am running TRACULA on free surfer 6.0.0 and have done the 1st and 2nd step and am getting stuck on the last step with the following error. Loading atlas reference volume from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz niiRead(): er

[Freesurfer] Recon Error

Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I have attached the log file. Any help is appreciated. Thank you, Emily Emily E. Rogers, MSc Wake Forest Graduat

Re: [Freesurfer] 7T recon

Hi Bruce, Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorpora

Re: [Freesurfer] Recon Error

Hi Emily no log file attached... cheers Bruce On Tue, 6 Jun 2017, Emily Rogers wrote: > Hello, > > I am trying to implement using Freesurfer segmentation in my analysis for MEG > data. I am trying to segment this structural MRI (1400composite.dcm) and I > keep getting errors. I have attached t

Re: [Freesurfer] 7T recon

Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote: > Hi Bruce, > Thanks again for your help so far. I've tried remov

[Freesurfer] (no subject)

Apologies-- This email contains attachment. Thank you. Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I hav

Re: [Freesurfer] (no subject)

mri_convert is having a problem reading 1400composite.dcm. It is not even recognizing it as a dicom. Where did it come from and what is in it? On 06/06/2017 04:35 PM, Emily Rogers wrote: > Apologies-- This email contains attachment. Thank you. > >

Re: [Freesurfer] (no subject)

It was converted to a single dicom from individual slice files using MIPAV image viewer. It is a single subject structural MRI. http://www69.zippyshare.com/v/MJDVstW0/file.html I've uploaded it here Thanks, Emily From: freesurfer-boun...@nmr.mgh.harva

Re: [Freesurfer] (no subject)

I don't think we can read that. Do you have access to the orignal dicoms? On 06/06/2017 04:58 PM, Emily Rogers wrote: > It was converted to a single dicom from individual slice files using MIPAV > image viewer. It is a single subject structural MRI. > > http://www69.zippyshare.com/v/MJDVstW0/fil

Re: [Freesurfer] 7T recon

Ah ok, thanks Bruce. Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfe

Re: [Freesurfer] (no subject)

I did not mean for you to send them to me. You should use one of them (any one of them) as input to recon-all On 06/06/2017 05:14 PM, Emily Rogers wrote: > Yes I have the original 160 files, attached. > > Thanks for your help, > Emily > > > > From: frees

[Freesurfer] recon-all: .md and .txt format

Yeah I do, I have read & write permission to that file, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] recon-all: .md and .txt format

Yeah I do, I have a read & write permission to that file. On Tue, Jun 6, 2017 at 11:03 PM, Douglas Greve wrote: > Do you have read permission to that file? > > On 6/6/17 3:45 AM, 곽유나 wrote: > > Hello FS experts, > > I ran recon-all, and got an error saying that it can't read certain txt > files

[Freesurfer] How to process ANCOVA with age as covariate

Hello FreeSurfer Developers,To compare cortical thickness between groups, I want to process analysis of covariance (ANCOVA) adjusting for age.When "mri_glmfit" process, do I insert "0 0 1 -1" in .mtx file?Would you please tell me how to process ANCOVA with age as covariate.FSGD FILEClass Group1Clas

Re: [Freesurfer] TRACULA (dmri_motion)

Hi John - You can read more on how to use the motion measures in our paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029882/ The gist of it is that it's not easy to set a hard threshold on the motion measures so that everything above the threshold is good data and everything below is ba

Re: [Freesurfer] TRACULA -path issue

Hi Katrina - Most likely the problem occurred earlier in the process, so the real error is hiding earlier in the log file. Can you please the entire scripts/trac-all.log file? Thanks, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.