Re: [Freesurfer] Deflate compression support

Jan Kalkus, Which version of freesurfer are you using? I think this problem appeared a couple versions ago and was fixed, so you may want to get the newest version. Nick > Hi, > > I'm using mris_make_template to create a template with some monkey > data. At the very end I get this messag

Re: [Freesurfer] make_average_subjects & FS v4.0.5

Antonio, If you have built your own average subject, then to use in qdec, you will have to do the following: 1) run 'recon-all -s -qcache -target myaveragesubj' where 'myaveragesubj is the name you gave to your average subject. by default, the -qcache command resamples the subject data onto th

Re: [Freesurfer] qdec

Judith, Does this message appear in the terminal? and otherwise not appear to have any other effect? That particular message can be ignored. I'm not sure what is meant by your two classes not being configured. Can you send me your qdec.table.dat file? Also, while not required, you should crea

[Freesurfer] Re: What's wrong in fmc.nii data?

Does that file exist? It looks like it is trying to load a bfloat file (ie, files with a bfloat extension). What format are your files in? > Hi all: > When I run selxavg3-sess on a analysis with 'fmc' as 'funcstem', the > program report the following error, > but when I did the same analysis

[Freesurfer] qdec

Hi. I am running qdec on freesurfer v 4.0.5. I am getting the following error messages: WARNING: Marker for class Main was invalid. WARNING: Color for class Main was invalid. My two two classes (male and female) are not being configured. I know from reading the freesurfer support lists that this

Re: [Freesurfer] Tutorial Example Data

Hi Amy, is there an aseg.mgz for subject2_before? If so, copy it to aseg.auto.mgz and you should be all set. We'll need to update the tutorial subject if this is the case. cheers, Bruce On Thu, 26 Jun 2008, Yuan Xu wrote: Hi,      I am new for FreeSurfer, and I am learning FreeSurfer tut

[Freesurfer] Tutorial Example Data

Hi,    I am new for FreeSurfer, and I am learning FreeSurfer tutorial now. I did some manual edit on subject subject2_before, then I ran the command: recon-all -autorecon2-wm -subjid subject2_before  I got error message as following:mri_fill: could not read segmentat

Re: [Freesurfer] brainmask.mgz vs. brain.mgz

Hi Petr, I would try to be consistent throughout the study, even if this means redoing some parts. cheers, Bruce On Thu, 26 Jun 2008 [EMAIL PROTECTED] wrote: Hi! Have a couple of questions regarding manual edits correcting the pial-surface. Have found out, in some of our data sets, that th

[Freesurfer] GTCA

Does anyone know if GTCA is part of the freesurfer commands? My protocol requires that I use a "GTCA" command to create a better surface image for stg. If not, can anyone direct me towards a resource to explain what it is and how to use it? Thanks. -- Daniel Horim Choi Northwestern University Cla

[Freesurfer] brainmask.mgz vs. brain.mgz

Hi! Have a couple of questions regarding manual edits correcting the pial-surface. Have found out, in some of our data sets, that the brain.mgz file has been used instead of the brainmask.mgz during edits to correct the pial surface. Seems that this protocol has been inherited from pre-version 3.

[Freesurfer] significance thresholds and multiple comparisons corrections

Hi FreeSurfer groupers. I have been using FreeSurfer since v3.0.2, but still have some questions about the group analysis pipelines. I have used both QDEC and the previous manual method using glm_fit. Questions about QDEC: 1. What are the guidelines for setting significance thresholds, by adjus

[Freesurfer] What's wrong in fmc.nii data?

Hi all: When I run selxavg3-sess on a analysis with 'fmc' as 'funcstem', the program report the following error, but when I did the same analysis on the same data with 'fmcsm6' as 'funcstem', the program could run successfully. our data was preprocessed with the command 'preproc-sess -sf cm_ses

Re: [Freesurfer] segmentation protocol for the hippocampus

Hi Nick, it's the protocol defined by the Center for Morphometric Analysis here at MGH. Dave Kennedy (ccd) can give you more details. cheers, Bruce On Thu, 26 Jun 2008, Nicolas Cherbuin wrote: Hi, Where can I find the protocol used to segment the hippocampus in freesurfer? I am comparing

Re: [Freesurfer] segmentation protocol for the hippocampus

Hi Nicolas, This week in Brisbane you can find some of the developers of FreeSurfer to discuss this issue. My thoughts are: manually traced hippocampi is a still open problem. In 1.5T in a good quality SPGR or even in 3T it's a difficult task and many times very operator dependant. In FreeSurfer