[Freesurfer] recommended WM lesion filling procedure?

Hi, I have a bunch of scans from patients with mulitple sclerosis. Since they all have substantial t2w hyperintensities I would like to automate the process of WM filling and re-running. Looking through the emails and the wiki, however, I am a bit confused. http://www.freesurfer.net/fswiki/FsTutor

Re: [Freesurfer] qdec cannot find subjects in qdec.table.dat

Hi, I am also having the same problems. Was this ever resolved? I run freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 on ubuntu hardy 2.6.24-18. thanks, mishkin On Wed, Sep 10, 2008 at 12:55 PM, David Qixiang Chen <[EMAIL PROTECTED] > wrote: > Hi, > I'm running freesurfer in Ubuntu hardy 2.6

[Freesurfer] qdec.table.dat error

Hi, When I try to load a qdec.table.dat I always get the same error: sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tri

[Freesurfer] qcache commands

Hi, I am trying to understand what happens when you run the recon-all -qcache command I noticed these three commands get run: mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg -

Re: [Freesurfer] qdec.table.dat error

gt; >> thanks, >> mishkin >> >> >> On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky >> <[EMAIL PROTECTED]> wrote: >> > Mishkin, >> > >> > Does this directory exist? >> > >> > /lab1/FreeSurfer/4.0.5/ms-mni/testing/test

Re: [Freesurfer] qcache commands

27;, as mris_preproc is used by the -qcache. In other usages > of mris_preproc, it is possible to concatnate multiple files. > > Nick > > > On Tue, 2008-10-07 at 17:16 -0400, Mishkin Derakhshan wrote: >> Hi, >> I am trying to understand what happens when you run t

[Freesurfer] lh.thickness file format

Hi, I have my own stats files that I would like to incorporate into the freesurfer stream, if possible. Ie. after running FreeSurfer, I create a ?h.mystats (containing something like image intensities for example), where the format of ?h.mystats is just an ascii file, where each line is the value a

[Freesurfer] recon-all -long questions

Hi, I have a couple questions regarding the -long option. 1) The longitudinal instructions listed in recon-all -help all use recon-all -all -long. If I am only interested in the subcortical segmentation, will the longitudinal processing still work if I only use recon-all -subcortseg ? 2) How long

Re: [Freesurfer] Segmentation Volume Data

Hi, Are the details of the partial volume corrections described anywhere on the wiki, I couldn't find anything? Is it just a certain percentage of the volume that is disregarded depending on the surface area, or is there a probabilistic labeling of the structures somewhere? Is it possible to get a

[Freesurfer] postmortem data

Hi, I have three questions regarding some postmortem data at high resolution (0.35 mm^3 isotropic). 1) A question was asked about the possibility of using postmortem scans in freesurfer back in sept 2007 and Bruce said: >Not easily, although we have some tools for doing this. They aren't packaged

Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

Hi Lloyd, I dealt with the same problem at one time. My input volume was a minc volume but I imagine the procedure should work for your input as well. for native.mnc, which was your input into freesurfer, do this command: mri_info --cras native.mnc my output was -2.35588 52.7907 24.8145 Then you

[Freesurfer] masking out ROIs on the surface

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in

Re: [Freesurfer] masking out ROIs on the surface

ate things. thanks, mishkin On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl wrote: > Hi Mishkin, > > yes, the ?h.cortex.label should be created for every subject that labels the > cortical regions of the surface. > > cheers, > Bruce > On Tue, 7 Apr 2009, Mishkin Derakhshan wrote: &

Re: [Freesurfer] masking out ROIs on the surface

    X       Y       Z       labelno > > where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for > instance 1007 is ctx-lh-fusiform > > Nick > > > > On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote: >> Thanks. After reading up on the wiki

Re: [Freesurfer] masking out ROIs on the surface

quot;> ${DIR}/${name}/label/${hemi}.annot.asc"); open(FTXT,"> ${DIR}/${name}/label/${hemi}.annot.txt"); foreach $element(@master){ my @array = split(/ /,$element); print FASC "$array[0]\n"; #names print FTXT "$array[1]\n"; #num

[Freesurfer] colin27 skullstrip problem

Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all complet

Re: [Freesurfer] colin27 skullstrip problem

you. > > cheers > Bruce > > > On Mon, 30 Nov 2009, Mishkin Derakhshan wrote: > >> Hi, >> I'm trying to get the surfaces for the colin27 brain that is included >> with the mni packages. Has anyone managed to do this before? >> >> I thought I would

[Freesurfer] subject to fsaverage

Hi, I am looking for the transformation matrix that takes my input volume (orig.mgh) and maps it into the same space as fsaverage (or the inverse of this transformation if it already exists). I've already run recon-all -all, and -qcache, so I'm pretty sure this information exists somewhere, but aft

[Freesurfer] error testing freesurfer installation

Hi, I just installed the rh9 version of fressurfer. I am running Ubuntu 6.10. I had the libtiff.so.3 error, which I seemed to have fixed by just making a sym link to libtiff.so.4 ( I hope that is okay). Now I get this error about the aseg.mgz.gz not existing. It looks like it isn't looking in the m

[Freesurfer] Coordinate Systems

Hi, I am new to FreeSurfer and even after having read the wiki, I have a few questions regarding the coordinate systems. 1. What coordinate system do the final surfaces have. ie. mris_convert rh.pial rh.pial.ascii will list the coordinates in what space? 2. Are the coordinates of T1.mgz and rh.p

[Freesurfer] subcortical segmentation

Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon

Re: [Freesurfer] subcortical segmentation

Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields a

Re: [Freesurfer] subcortical segmentation

4.0000 Mishkin Derakhshan wrote: Hi Jenni, thanks for the reply. The log file says it finished without any eroors. In the aseg.stats file, none of the structures have the NVoxels of Volume_mm3 reported. I attached the file so you can see what I mean. I am using freesurfer-Linux-rh9-stable-pub-v3.

Re: [Freesurfer] Ubuntu and freesurfer

I am currently running freesurfer on Ubuntu, so yes! Ubuntu runs Debian linux, so you can just follow the instructions for a debian install located on the wiki (ie. use the Red Hat 9 download): http://surfer.nmr.mgh.harvard.edu/fswiki/Download mishkin p.s. Perhaps Ubuntu can be added to the list

[Freesurfer] mri_convert options

Hi, I am having troubles getting the right options with mri_convert. I ran: recon-all -autorecon1 -i original.mnc -s subj1 recon-all -subcortseg -s subj1 I now want to convert aseg.mgz into aseg.mnc but in the same space and with the same orientation as my original.mnc file. My original.mnc file

Re: [Freesurfer] mri_convert options

arg original.mnc \ > --o aseg-in-native.mnc \ > --regheader \ > --interp nearest > > Nick > > > On Thu, 2007-12-13 at 22:05 -0500, Mishkin Derakhshan wrote: > > Hi, > > I am having troubles getting the right options with mri_convert. > &

[Freesurfer] right choroid plexus missing

Hi, Is there any reason why aseg.stats only has a label for the left-choroid-plexus (id 31) and none for the right? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] Hardware

Hi, I currently run a CPU with 2 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz with 16GB RAM, and a single instance of recon-all -all with version freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 takes this long: real1219m45.802s user1218m32.345s sys 2m1.152s Which is about 20.5 hours. In my

[Freesurfer] surface co-ordinates

Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? 2. I am making the assumption that the lh.white and the lh.pial will always have the same number of indices and polygons. Can

Re: [Freesurfer] surface co-ordinates

On Wed, Feb 20, 2008 at 10:46 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > On Wed, 20 Feb 2008, Mishkin Derakhshan wrote: > > > Hi, > > > > 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate > > system are the xyz co-ordinates reported in?

Re: [Freesurfer] WM mask

HI Antonio, You can use mris_convert to get the surfaces into ascii format. ie: mris_convert lh.white lh.white.ascii If you look at the file you see the following: #!ascii version of lh.white 126302 252600 -7.101086 -100.61 -1.796945 0 -7.231718 -99.740860 -1.915022 0 . . -7.355780 53.0

[Freesurfer] inflation and registration to a sphere

Hi, After reading the wiki and the references on the wiki, specifically [1] and [2], I'm still a little confused about how the inflation and registration to a sphere occurs. ie. what energy functions are being minimized at each step. I think it is a 3 step process, where 1. Surfaces are inflated

Re: [Freesurfer] Calling mri_convert from Java code

Hey Alex, Just from looking at the first two lines of your environment variables I think you might have forgot the 's' on Applications for FREESURFER_HOME. >>> String[] env = {"FREESURFER_HOME=/Application/freesurfer", "FSFAST_HOME=/Applications/freesurfer/fsfast", mishkin On M

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

Hi Lucia, I ran into the problem as well. For me, just making a symbolic link named libtiff.so.3 which points to libtiff.so.4 seemed to do the trick. Try this: ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 (assumes your libs are in /usr/lib/) hope that helps, mishkin On Sat, Mar 29, 2008 at 9

Re: [Freesurfer] cortical surface in MNI space?

Hi David, I use both the MINC world and the freesurfer world. One thing which may be of use to you or others, is to get from the surface co-ordinates, back to world-coordinates (or "scanner RAS"), so that minc tools etc. display things properly. To do this, you need to apply a simple translation.

[Freesurfer] vertex correspondence

Hi, I know that at some point in the pipeline, the surfaces are registered to a common sphere, and thus I'm hopping there is a one-to-one vertex correspondance between subjects. My question is, let's say I look at vertex X, on subject1, how do I find out the corresponding vertex location on subje

[Freesurfer] ASEG atlas modality

Hi, >From what I read here: https://surfer.nmr.mgh.harvard.edu/fswiki/AsegOptimization The atlas has is made from 27 data sets (14 GE, 13 SIEMENS). Can you give a bit more info about the sequences used. ie were they FLASH-based or MPRAGE. Are these 27 data sets available for download somewhere?

[Freesurfer] 3mm slices?

Hi, I'm wondering if anyone has looked at the accuracy/reproducibility of cortical thickness measurements using 3mm slice data. I found the Han 2006 paper in NeuroImage comparing different sequences, but it doesn't compare different slice thicknesses. If not, does anyone have anecdotal experience u

[Freesurfer] wm edits to fix memory error

I don't think this made it through to the list the first time... Hi, Like others on the list I got the ran out of memory error, which seems to be the result of a gross error somewhere: CORRECTING DEFECT 1 (vertices=109084, convex hull=14490) Excessive topologic defect encountered: could not allo

[Freesurfer] qdec with custom paths?

Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23