[Freesurfer] FW: difference # vertices in sphere

To: Kirk Gregory R. Subject: Re: Help Deepti with some questions Dear Greg I have been looking at FreeSurfer data provided by you for 21 subjects(AD/Control). For P1_AD subject I found the # of vertices of sphere file different from the length of thickness data for the same subject. # of vertices

[Freesurfer] segmentation fault

Hi all, I got in the recon-all log #...@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009 /home/gkirk/freesurfer/freesurfer/subjects/P21/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance P21

RE: [Freesurfer] segmentation fault

Sent: Wed 5/13/2009 3:39 PM To: Kirk Gregory R. Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] segmentation fault Greg, How much memory does the system have available at the time mris_volmask is run? It will consume about 1GB within a minute or two of starting, and I know

[Freesurfer] mri_convert crash

I have epi data with a single slice at each time point and am trying to convert it. get MRIresample(): error inverting matrix; determinant is nan, matrix is: when it tries to resample the data. seems the single slice blows a fuse. i don't see a flag to turn off the resampling ? or other way

[Freesurfer] GE 3T protocol

Hi, can anyone suggest a 1mm isotropic T1 protocol they feel is fairly well optimized for freesurfer for a pre mr750 GE 3T scanner. seems Andre used to have such a list, or was it just for the siemens scanners. thankx Greg. ___ Freesurfer mailing

[Freesurfer] apple leopard 64 bit

Hi all, Are there plans to release binaries for the Mac Leopard 64 bit Greg. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] hardware for computing Q for Paul Raines

Hi Paul, We have been plowing a lot of data with freesurfer, FSL, etc. and are thinking of moving up to a hunkier computer system, anything from 4 processor workstation to a minimal cluster. Wonder if you know a couple URL's of stuff you equipment you think is decent for a starter system G.

[Freesurfer] old Mac ver.

Hi, I have a radiologist that wants to do some freesurfer work, visualizing subcortical parcelations and orig and T1 volumes. The volume processing was done with freesurfer-v3.0. Can I install the current freesurfer-Darwin-tiger-stable-pub-v4.0.1-full.dmg and have it correctly visualize the

[Freesurfer] significance in unknown region

Hi All, I have wondered what is done in the medial and inferior region where a patch needs to be put across to seal each of the two hemispheres. The variables , thickness etc... have some value in the region as we see a representation on the thickness maps. Is something like averaging with a

[Freesurfer] mean thickness difference maps

Hi All, I wanted to clarify a point. Publications of cortical thickness differences are usually produced with maps called mean thickness difference maps. I dug through the mail archive but did not find an answer (Q1) These statistical parametric maps are I assume produced by computing a

[Freesurfer] xform avesurf- subject

Hi All, I want to click on a point on my average surface for my group and ' save point' load a T1 or orig subject in the group with tkmedit and 'goto saved point' i.e. map by the inverse of the transform that embeded the subject surface into the average surface and see the point on the

[Freesurfer] design matrix Q ?

Hi refering to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DesignMatrix Design Matrices with DOSS and DODS I want to make an analysis of same offset different slope between classes with a continuous age variable If I was doing this with the example( 3 variables ) starting with

[Freesurfer] qdec for old ?

Hi , I would imaging we would need to be running the most recent freesurfer version to use qdec We just finished a study with V3.0 and are doing the analysis. Mainly interested to see if we could do some analysis with subcortical structures. thanks Greg.

[Freesurfer] manual edit problem

Hi, I am trying to fix the few subjects in my study ( 3 of 64 ) that need manual fixes resulting from skull strip erros ( 2 of 3 cerebelem was left out ). This is the first study since my student who was doing this for me left ... So the note he left said do tkmedit practice/subjectname/

[Freesurfer] scan res

Hi, If I did a good job looking through the maillist archive the use of scans with resolution less than 1mm is not handled automatically yet, i.e. have to manually normalize ( divide ) quantities so the numbers are correct. Since we can only get a tiny bit less than 1mm ( 0.9mm ) for patient

[Freesurfer] 3T sequence

Hi, we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this

[Freesurfer] credits for talk

Hi Folks, I remember somewhere there was a page describing how we should put the credits for a publication. How do you want the credit to read for a clinical conference talk reporting freesurfer cortical thickness group study results G. ___ Freesurfer

[Freesurfer] imaging and neuropsych intervening time

Hello all, We are doing studies correlating neuropsychological measures of executive function in normal and clinical populations, epilepsy and sickle cell disease. I am looking at the issue of the amount of time allowed between acquiring the volumetric MR and performing the battery of

[Freesurfer] NIfTI format conversion

Hi All , I am using mri_convert to convert Siemens 30 direction diffusion data into NIfTII for proc. with fsl. mri_convert does it well except that it is a bit problematic that it comes out in neurological convention. Also the tools is fsl do not seem capable to change the orientation to

[Freesurfer] mri_convert SC dicom

Title: mri_convert SC dicom Hi folks, I was trying to convert an dicom MPRAGE with a SISCOM activation( grayscale ) to nii format to use the activation for a seed for probalistic fiber tracking. The siscom is created in Analyze(program not file format) and then exported to dicom , so it

[Freesurfer] resampling spm2 activations

Title: Message Hi, I think this is one for Doug, Thomas Witzel told me it is possible to resample the volume activation data from spm2 onto the cortical surface generated with freesurfer. Is their a blurb around that details the process or could you give me some instructions. thanks

RE: [Freesurfer] GNU GPL source?

It would be nice whatever could be available for having a detailed look At what some of the code does. Also for persons anticipating trying To do some algorithm work a bit of perusing the code to having a working Understanding would be interesting. Also maybe feedback on what parts of the Code are

RE: [Freesurfer] cortical thickness in freesurfer

While on the subject of cortical thickness. Looking at the new tutorial there is an expanded section on cluster analysis. If my reading is correct the best way to get P values for a study is to do the cluster analysis on the group analysis results and use the P value bounds obtained As a result

[Freesurfer] overlay thickness maps

Title: Message I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented from the tutorial/tutorial group study tried tksurfer subject lh inflated - got the gray surface next file-load overlay -

[Freesurfer] defining labels

Title: defining labels Hello, I remember a message from Bruce to use mris_anotomical_stats -l label to generate statistics for a region, but unfortunatly I cannot find how to define a label, docs do not seem to tell, a quick start tip please. G.

FW: [Freesurfer] thickness measures

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kirk, Gregory Sent: Tuesday, March 15, 2005 1:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] thickness measures Hi I would like to know if anyone has much experience doing pediatrics

RE: [Freesurfer] thickness measures

Hi I would like to know if anyone has much experience doing pediatrics with freesurfer. I was able to get what look like good results from a 2 year old and a 16 year old, the surfaces look good with only automated topology fixing. An 8 year old needs a lot of manual work. The +- on the cortical

[Freesurfer] thickness measures

Title: thickness measures HI all, wrt useing freesurfer for obtaining cortical thickness there are the lh.thickness etc. and the theoretical paper in the citations, but I have not found things that would show me how to derive things like, average thickness for an individual, average