Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

recon-all -make all error?
by Jeff Sadino 06 Dec '10

06 Dec '10

Hello, I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am doing this by issuing the "recon-all -make all -s subject" command. It stops right away with the message: make: Nothing to be done for `all'. There exists the wmparc.stats file from the fs450 recon, but there is no label/?h.BA*.label or label/?h.entorhinal_exvivo.label files. Looking at the recon table, it looks like these are supposed to be part of the standard recon. Is my -make all broken, or can I ignore this message? Thank you, Jeff Sadino

1 0

RAW files
by Alan Francis 06 Dec '10

06 Dec '10

Hi FSL and FreeSurfer folk: Does anyone know how to convert *.raw files to analyze, nifti or mgz format? thanks much, Alan

2 1

mri_convert batch conversion of ima files
by Lisa F. Akiyama 06 Dec '10

06 Dec '10

Hello, I have a large number of slice files in ima format. I would like to convert each of these ima files into either nifti or analyze format slice files. I read a past email conversation regarding batch conversion of ima files using mri_convert : https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010524.html However, when I ran the following commands, I get a single nifti/analyze file that contains all the slices for this particular subject. Is there a way to batch convert all ima slice files to individual nifti/analyze files? I read somewhere about the --sdmlist option, but that did not work. Thanks. Best, Lisa *<ima -> analyze>* > todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.nii... > todd@neptune-ubuntu:/usr/local/freesurfer/subjects/kikuchi_hiromi/slices$ > mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img > mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.img... > Analyze Output Matrix > -0.000 -0.000 -1.500 87.097; > -1.000 0.000 0.000 114.029; > -0.000 -1.000 0.000 118.726; > 0.000 0.000 0.000 1.000; > -------------------- > No such orientation specified in Analyze7.5. Set orient to 0 > Direction cosines for > /usr/local/freesurfer/subjects/kikuchi_hiromi/slices/393-2-4.ima are: > x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -4.4032 > x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = -14.9706 > x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -10.2740 > INFO: set hdr.hist.orient to 'transverse unflipped' > > *<ima -> nifti>* > todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.nii... > ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

2 3

Using mri_segstats
by Tyler Blazey 06 Dec '10

06 Dec '10

Hi, I have two questions about using mri_segstats. First, I notice that on the individual dti tutorial, you don't use the --pvol option to correct for partial voluming. Is there a reason for this? Second, would there be any disadvantage to using mri_segstats with aparc+aseg.mgz to get volume/ thickness measurements? I know from the ReconAllDevTable that the standard method is to use mris_anatomical_stats, but I need to get the stats after transforming the aparc+aseg image, so that is not an option. Thanks for any help. - Tyler

2 1

To use the file thickness.mgh outside Freesurfer
by qizhu wu 06 Dec '10

06 Dec '10

Dear experts, I am greenhand for using FS, and am looking for ways to use the FS generated parameteric files, such as *thickness.mgh, *sulc.mgh, etc, outside FS. I got the following questions: 1. Whether these files contain coordinate information for each vertex, so I can transform them into image style file? If they do, that'll be very helpful. 2. If these files could not be tranformed into images, I am going to tranform them into ascii files using FS commands. The questions is: what's the orgnization of the output ascii file? i.e., from where to where inside the file is the header information, and does each line in the file stand for the value of a single vertex? How can I make such a ascii file which contains only vertex values in the right order? 3. I have obtained ascii files of individual's cortical thickness using mri_convert (with header inside), however, when I open it using different tools, the values look different, why? Best wishes Qizhu Wu HUaxi MR research center West China Hospital, Sichuan University

2 1

fsaverage triangle mesh data
by Ørjan Bergmann 06 Dec '10

06 Dec '10

Dear all I am interested doing some visualization of my cortical FreeSurfer results in other software. In order to do so I need to some information about how the cortical surface is defined. Usually these surfaces consists of a set of 3D coordinates which gives the position of the vertices (163842 in the case of fsaverage), and a set of triangle definitions which are 3 indices into the vertex data (see http://en.wikipedia.org/wiki/Triangle_mesh ) Is it possible for me to access the triangle and vertex information of the cortical surface of the fsaverage subject? --- Sincerely Ørjan Bergmann, PhD Post. Doc. University of Oslo

4 3

Create a surface from fMRI data
by Leonardo Barbosa 05 Dec '10

05 Dec '10

Hello, I've been looking through the tutorials and this list but couldn't find the answer: is it possible to create a surface from fMRI data *without* the anatomical MRI data? I know I can use mri_vol2surf but it needs a "subject" parameter, so I need to run recon-all before to create the surfaces, right? Is it possible to create a subject and surfaces (spherical, etc) with only the fMRI data? Thanks in advance for any help! Leonardo Barbosa Insituto de Física da Universidade de São Paulo if.usp.br

2 3

funcroi-table-sess
by Yuko Yotsumoto 05 Dec '10

05 Dec '10

Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. With v5.0, those commands do not seem to work. I could get a table with: > funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -contrast all_null -sign abs -thresh 1 -force > funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 > funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh -c all_null However, what I want is BOLD values in each time point for all conditions. funcroi-table-sess fails if I do not specify a contrast. > funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -force > funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 > funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh ERROR: must specify a contrast Is there a command that gives me values, not a table? Thank you, Yuko

2 2

control points-- Any tips?
by Deniz Ozgen 03 Dec '10

03 Dec '10

Hello, I have about 10 subjects that I am trying to obtain cortical segmentations. In some of the cases parts of the temporal lobes are not included in the segmentation due to low intensity (or RF bias). I tried adding control points as described in the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints) The wm/pial boundaries are worse than before, excluding even more parts of wm, even where I placed the control points. I added about 30-50 controls points mostly in low intensity wm strands that are not correctly segmented. I was hoping someone may have some tips or hints on good placement of control points, besides the ones on the tutorial. Trial and error is suggested in the tutorial but considering the time it takes to re-run each subject, it is too time consuming. Thanks in advance. Deniz Ozgen.

2 1

Saving individual slices within a nifti file
by Lisa F. Akiyama 02 Dec '10

02 Dec '10

Hello, Is there a way to individually save slices within a nifti file in the nifti format using the mri_convert command? Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

2 4

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2010