Freesurfer October 2004

freesurfer@nmr.mgh.harvard.edu

27 participants
37 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

FsFast file conversion/preprocessing
by Margaret Duff 01 Nov '04

01 Nov '04

Hi, I have 12 runs of functional data I am trying to convert to FSFast formats and then preprocess. I have been using mri_convert to make my .img files into bshorts. However mri_convert makes only 30 files when my folders originally contained 37 or 73 files. Is this what it is supposed to do? I am also then trying to run preproc-sess on these files but i keep getting an error during the motion correction of the first run. it says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf sessid -df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank you so much, Margaret Duff

2 1

filling the white matter
by Wan Park 01 Nov '04

01 Nov '04

when I run recon-all -s uf1 -talairach (uf1 is the subject) I receive this message: $ ####################################### INFO: SUBJECTS_DIR is /Volumes/stem/freesurfer/subjects --------------------------------------------- Talairach Fri Oct 29 17:23:19 ADT 2004 /Volumes/stem/freesurfer/subjects/um1/mri talairach2 um1 INFO: registering um1 Fri Oct 29 17:23:19 ADT 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /Volumes/stem/freesurfer/subjects/um1/mri/transforms/talairach.xfm /Volumes/s m/freesurfer/subjects/um1/mri/orig /Volumes/stem/freesurfer/subjects/um1/mri/orig Fri Oct 29 17:25:26 ADT 2004 INFO: starting per-hemisphere operations ----- Starting Hemisphere rh -------- ----- Starting Hemisphere lh -------- ------------------------------------------- recon-all finished without error at Fri Oct 29 17:25:26 ADT 2004 done but when I return to csurf and I try to create the surface, I receive this message when it is filling the white matter: area[0] = 2 (min = 350, max = 790), aspect = 2.00 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished Could you tell me what to do? Thanks Wan

3 2

what the qsurfer can show
by Joongnam Yang 31 Oct '04

31 Oct '04

I ran qsurfer -stat thresh_zstat1 -subject ID -hemi lh -old and got the image displayed. But the image is structural image only. I thought that the above command shows the anatomical and functional data overlaid. Am I wrong? Or how can I see the two data overlaid in one image? Thanks in advance Nam.

1 0

Re: [Freesurfer] MNI auto talairaching
by Joongnam Yang 29 Oct '04

29 Oct '04

I've got an error message when I was running "mri_vol2surf" file mri/transforms/talairach.xfm not found I guesss I need to do talairach transform, Could someone please tell me how to do it? Nam.

3 2

Re: [Freesurfer] MNI auto talairaching
by Joongnam Yang 29 Oct '04

29 Oct '04

>>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/29/04 2:16 PM >>> In general, you should not need a talairach transform to run mri_vol2surf, but I can't tell what you're trying to do -- no command-line :(. If you need to talairach, then you can run: recon-all -s subjectid -talairach Joongnam Yang wrote: > > I've got an error message when I was running "mri_vol2surf" > > file > mri/transforms/talairach.xfm > not found > > I guesss I need to do talairach transform, Could someone please tell me how > to do it? > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

1 0

MNI auto talairaching
by Wan Park 29 Oct '04

29 Oct '04

could you please tell me how to do auto talairaching with the MINC? thanks wan

1 0

tkregister2 question
by George Papadimitriou 27 Oct '04

27 Oct '04

I am trying to register a lowb volume to an average volume. In this particular case, I'm trying to use tkregister2: % tkregister2 --targ avg_000.bfloat --mov indivsubj_000.bfloat --reg \ register.dat I am having a problem with the brightness of the TARG volume. It seems to be set near ~1, and using the fmov option only adjusts the brightness on the MOV volume. It is kind of hard to align them, when the target volume looks like a binary mask (appears all white). Have you seen this before? Changing the contrast doesn't seem to help. Thanks, George P.

2 2

when I am creating the surface
by Wan Park 26 Oct '04

26 Oct '04

I start with the filling of white matter but after a while I am receiving this massage: (...) using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished could you help me with this? thanks, wan park

4 3

segmentation fault during fill step
by Jason 25 Oct '04

25 Oct '04

The white matter surface creation step resulted in a poor L/R hemisphere separation in one of my subjects. A portion of the cut is shifted into the left hemisphere white matter (running from the corpus callosum downward to the brain stem). To remedy this I ran the following command to manually set the corpus callosum cutting planes: recon-all -subjid pbb_subj.07 -fill -cc-xyz 131 125 146 I encountered the following error: Searching for cutting planes.Segmentation fault (core dumped). Can you offer me any advice on how to remedy this problem? Thanks, Jason

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2004