Re: [Freesurfer] Freesurfer Start Up

Hello Bruce, I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command: tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_da

Re: [Freesurfer] license file not working

what version of Linux are you using? On Fri, 1 Aug 2014, Saemann Philipp wrote: Hello Douglas, the file created on Linux, no Windows involved, and was 100% identical to the old license file that was successfully used for some time. Do I need a new download? Thanks, Philipp At 16:14 01.08.2

Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

you could get a T2 or FLAIR and use it to fix the pial surface On Fri, 1 Aug 2014, McLaughlin, Katie wrote: > Hi Andre and Bruce, > > Thanks for your input here. The sat band has helped, although it hasn't > entirely corrected the problem (the image attached was from a subject with > the sat b

Re: [Freesurfer] QDEC Cluster Analysis

Thanks Doug. On Aug 1, 2014 4:16 PM, "Douglas N Greve" wrote: > > On 07/31/2014 03:16 PM, Mohammed Goryawala wrote: > > Hello All, > > > > I have some questions related to the qdec analysis I have run. > > > > 1. On running the qdec I see that FWHM is an input which changes > > cluster definition

Re: [Freesurfer] GLM error in QDEC

Hi Doug, Same error when data table created in Linux There are a number of messages about this same issue in the Archive (e.g.): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033471.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html http

Re: [Freesurfer] GLM error in QDEC

How did you create your qdec table? It looks like it might have been created on a windows machine. If so, try creating it in linux. doug On 08/01/2014 04:53 PM, McLaughlin, Katie wrote: > Hi Doug, > > The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR > (see output belo

Re: [Freesurfer] GLM error in QDEC

Hi Doug, The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR (see output below) when loading the data table. The subjects are all in the directory, however, with permissions set to 777 on all. I've found a number of previous posts with the same error, but no solution.

Re: [Freesurfer] license file not working

Hello Douglas, the file created on Linux, no Windows involved, and was 100% identical to the old license file that was successfully used for some time. Do I need a new download? Thanks, Philipp At 16:14 01.08.2014 -0400, you wrote: > >not sure what is going wrong. How did you create the file? M

Re: [Freesurfer] license file not working

not sure what is going wrong. How did you create the file? Make sure it is a simple ascii text file not created under Windows On 08/01/2014 04:10 PM, Saemann Philipp wrote: > Hello users or support team, > > after using FS successfully for some time, now, after > a trivial command such as > > m

Re: [Freesurfer] holes in inflated using mris_label2annot

what was your command line? On 07/21/2014 03:43 PM, April Clausen wrote: > Hi Dr. Greve, I tried to upload the images with the Martinos Centre > Dropbox but I could not activate the dropbox … so the images are > attached. The 6 labels and annot file were created on fsaverage and > the image sho

Re: [Freesurfer] QDEC Cluster Analysis

On 07/31/2014 03:16 PM, Mohammed Goryawala wrote: > Hello All, > > I have some questions related to the qdec analysis I have run. > > 1. On running the qdec I see that FWHM is an input which changes > cluster definition significantly. How would I choose the right FWHM > for the analysis and can

[Freesurfer] license file not working

Hello users or support team, after using FS successfully for some time, now, after a trivial command such as mri_convert -it analyze T1.img -ot mgz 001.mgz an error appears as follows: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from T1.img... -

Re: [Freesurfer] grey matter density

We don't compute density. You can run mri_compute_volume_fractions to produce such images doug On 07/31/2014 09:54 PM, Qiongmin wrote: > Dear All, > > I wonder if there are any functions that can calculate the grey matter > density of the vertices or in the ROI manner? I figured out that Free

Re: [Freesurfer] GLM error in QDEC

So, did it generate the error when you loaded the table or when you hit analyze? List the steps and buttons that produce this error. doug On 07/31/2014 05:20 PM, McLaughlin, Katie wrote: > Hi Doug, > > I'm using 5.3. > > This error was generated when I had more variables in the model, so I used

Re: [Freesurfer] FW: YANQ follow-up

Hi Don, try looking at this page for more info on our coordinate systems https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 08/01/2014 10:47 AM, Bruce Fischl wrote: > Hi Don > > the -rt nearest switch is for mri_convert. I'll leave the rest of the > questions for Doug :) > Bruce >

Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

Hi Andre and Bruce, Thanks for your input here. The sat band has helped, although it hasn't entirely corrected the problem (the image attached was from a subject with the sat bands included). We are using a local transmit coil. I'm going to check with our physicist about the inversion pulse -

Re: [Freesurfer] Checking Back In: FLAIR Registration Problems

Hi Marta, I thought I was going to be ready to release it today, but my checks failed on the new script, so now I have to dig into it to see what is wrong. Check back next week. doug On 08/01/2014 09:19 AM, Zamroziewicz, Marta Karolina wrote: > Good morning, > > I’m just checking back in about

Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

Hi, Thanks, yes, we have this problem on our scans from the Allegra and 7 T scanners, where there's a local transmit coil (no body transmit coil) and therefore blood with non-inverted spins enters the head after the inversion pulse and appears bright in the images. With our Allegra scans this

Re: [Freesurfer] Editing the pial surface

Hi Lindsay, not really. It would be pretty hard to do, particularly if the topology isn't right sorry Bruce On Fri, 1 Aug 2014, Lindsay Gubernick wrote: > Hi, > I am doing manual corrections of topological errors and am wondering if > there is a way to bypass recomputing the surfaces as sugges

Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

Hi Kate I'll cc Andre and Dylan, but I would have thought some sat bands in the neck would do it. I think vessels are usually bright in the mprage, but don't usually case problems. Comments welcome cheers Bruce On Fri, 1 Aug 2014, McLaughlin, Katie wrote: Hi Doug, Bruce, et al. We'

[Freesurfer] Editing the pial surface

Hi, I am doing manual corrections of topological errors and am wondering if there is a way to bypass recomputing the surfaces as suggested by the topographical errors tutorial and instead doing some sort of manual editing of the pial surface. Does such an editing option exist? Thank you, Lindsay

[Freesurfer] Help with mris_convert

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label aft

Re: [Freesurfer] GLM error in QDEC

Hi Doug, Just wanted to follow up on this. I'm getting the error that says that the QDEC GLM design creates 0 factors, regardless of how many of the factors in the data table I sent are included in the design. (There are a total of 2 discrete and 9 continuous variables in the data table.) I

Re: [Freesurfer] FW: YANQ follow-up

Hi Don the -rt nearest switch is for mri_convert. I'll leave the rest of the questions for Doug :) Bruce On Fri, 1 Aug 2014, Krieger, Donald N. wrote: Thanks for posting back so quickly, Bruce, and for the direction.   Just to clarify, here is the command which I am using so you can see th

[Freesurfer] trac-all -prep problem

Hi Freesurfer experts, I ran the command on a bunch of subjects and all of them finished in ~90 minutes except one. This subject keeps on going into a seemingly endless loop. It has been running for almost 12 hours now. A section of the console output is reproduced below. What is the issue here

Re: [Freesurfer] FW: YANQ follow-up

Hi Don try mri_label2label. Also, the if you are transforming label volumes you need to use nearest neighbor interpolation, so include the -rt nearest switch. cheers Bruce On Fri, 1 Aug 2014, Krieger, Donald N. wrote: Hi All,   I am still in need of finding the tool sequence to generate

Re: [Freesurfer] recon-all.log error: "_FindFacePath: could not find path!"

Hi Alejandra sorry, that's a bug we fixed in 5.3. You need a new version of mris_topo_fixer and mris_fix_topology cheers Bruce On Fri, 1 Aug 2014, Alejandra Machado wrote: Hi, i'm a novel freesurfer user and i'm afraid i need some help here, please! ---

[Freesurfer] Checking Back In: FLAIR Registration Problems

Good morning, I’m just checking back in about a bbregister problem that I posted about earlier this week (see email below). I was told to check back at the end of the week about a patch. Thanks so much for your time and assistance! Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Labo

[Freesurfer] FW: YANQ follow-up

Hi All, I am still in need of finding the tool sequence to generate an ASCII file containing (1) voxel RAS coordinates (2) for a specific label (3) using the original MRI coordinates rather than freesurfer coordinates. mri_convert -rl rawavg.mgz does generate a new output volume cont

[Freesurfer] recon-all.log error: "_FindFacePath: could not find path!"

Hi, i'm a novel freesurfer user and i'm afraid i need some help here, please! - FREESURFER_HOME: /usr/local/freesurfer-5.1 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0