Freesurfer May 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
74 discussions

editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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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

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Intel Mac
by Ray Fix 19 Aug '06

19 Aug '06

Hello, Any plans for a Mac OS X Tiger Intel release? Ray

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Some FS input questions
by Graham Wideman 02 Jun '06

02 Jun '06

Most likely to Nick S, unless anyone else would like to chime in... I'm gearing up for some extensive use of FS... it's downloaded, installed, and initial tests run OK... so far with minimum of pain (yay team!). Now... I need to discover how to feed in data other than raw scanned files, because we want to try several alternatives to the initial processing, which we have in AFNI format, ac-pc aligned with iso-sided voxels but not 1 mm. I suspect I'll end up scouring the recon-all script, but a few hints would be helpful, mainly aimed at (a) taking advantage of processing that we have done by other methods, (b) minimizing resampling and (c) winding up with surfaces and segmentations that are most readily overlayed with our other processed data, tracings etc. 1. If we want to feed in already ac-pc aligned, brain-extracted input, at what stage of recon-all should we be looking to supply it? (I can figure out where in the directories to put the data, but not sure on the stage of processing to start at). 2. It used to be that FS's surface pipeline didn't insist on Talairaching the voxel data, and skipping that resulted in output that is true to original space. Is that still the case? 3. Does current FS proper require 256x256x256 1mm data, or can it take any shape "brick" and voxel size (ie: without resampling) these days? 4. If FS *does* want to work with 1mm voxels only: It used to be that though FS wanted 1mm input voxels, you could feed in some other sizes by do-it-yourself creation of the COR images, and FS was fine... is that still the case (but now with mgz format)? 4. Is it the case that the subcortical voxel-based parcellation *does* require the Talairaching step for correspondence with the probability atlas? 5. The surface and voxel-based pipelines are separate, not even sharing the white segmentation step, right? Thanks in advance, Graham

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question about flattening surfaces
by adam walczak 31 May '06

31 May '06

Hello, I was searching through the wiki and ran across a page that said to use csurf to make full surface cuts in order to ultimately create flattened surfaces. But while perusing the support archives, it was said that csurf is no longer supported. Is this true? How then do you make the full surface cuts needed to create the flattened surfaces? Thanks Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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mghWrite failure in mri_remove_neck
by Graham Wideman 30 May '06

30 May '06

Folks: In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that: 1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz 2. But then appeared to perform the neck removal anyway and write the output 3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz ... and sure enough, there is no such file there. The recon-all.log for these steps is copied below. This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory. I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for? But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it). Clues? Thanks, Graham =============== #-------------------------------------- New invocation of recon-all Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ####################################### [...] #@# Remove Neck Mon May 29 03:13:29 PDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006

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brain stem elimination
by Joongnam Yang 30 May '06

30 May '06

Hi all, I ran 'process volume' and 'create surface' and found that brain stem was attached to the left inflated brain. So, I editted 'wm' slices and got rid of the parts related to the brain stem in all slices. and ran 'create surface' again, but no change took place in the 'inflated brain'!!! Would someone suggest a solution to this? p.s. I ran 'recon-all' but it didn't make a difference, either. Nam.

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Reconstruction -> cortical maps without using Talairach transform
by adam walczak 30 May '06

30 May '06

Hello, I want to make cortical surface images that we will overlay with our own masks. But we want to do this in native space. So, I was wondering if it is possible to go thorugh the reconstruction process to make the surfaces without ever using the talairach transform and keeping everything in its native space. Thank you, Adam adam --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.

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problems with group analysis (mri_glmfit?)
by Lars M. Rimol 30 May '06

30 May '06

Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right? Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong? There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial: [lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt--glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731 $Id: mri_glmfit.c,v 1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done ------------ This is my FSGDF: $ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ -- yours, LMR

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mri_vol2surf problem
by adam walczak 30 May '06

30 May '06

Hello, I am trying to overlay my own ROIs onto the pial surface using mri_vol2surf. this is my command line: mri_vol2surf --src wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u --src_type analyze --srcreg wrawKH_MAE3_4/register.dat --fwhm 3 --hemi lh --surf pial --surfreg /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial --out wrawKH_MAE3_4/surf/lhpialoverlaytest --out_type paint --trgsubject wrawKH_MAE3_4 and this is my output: INFO: output format is paint srcvol = wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u srctype = analyze srcreg = wrawKH_MAE3_4/register.dat srcregold = 0 srcwarp unspecified surf = pial hemi = lh trgsubject = wrawKH_MAE3_4 surfreg = /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial interp = nearest float2int = round INFO: float2int code = 0 INFO: reading as a two-file NIFTI INFO: using NIfTI-1 sform Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial MRISread(/cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial): could not open file No such file or directory mri_vol2surf: could not read surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial No such file or directory the program seems to read the input images correctly, but can't read the surface images. I don't know what is up with the 'subject-unknown.' I specified the subject and it still doesn't know the path. I am kind of at a loss. Adam adam --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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Freesurfer May 2006