Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

feat2surf
by Strien, N van 31 Jan '06

31 Jan '06

Hi, I am having several problems with the feat2surf script when using this on my own data. For privacy purposes I renamed my subject to bert, however this refers not to the sample dataset: The problems that I face with the feat2surf script are as follows: 1) If I do not edit the script manually it stops when not finding a data file (zstat1.img) in analyze format. If I edit the feat2surf script so it only finds a zstat1.nii file it continues. 2) Results are not stored under 4 new subdirectories in the .feat main directory (as suggested in the tutorial). They are stored (and overwritten) in the /root directory. (I know it’s a bad habit of mine to work under the root account, but I expect the outputdir will only change to /home/$username/ if I change user. Ẃhen the script only looks for .nii files (and finds them) it exits nicely (after commenting away some of the images the feat2surf script looks for such as cluster* and rendered*). 3) When opening for example the rh volume in tksurfer, I get an error message that the .mgh volume is incorrect. This is the output when I run the feat2surf script without editing it. Mon Jan 30 13:32:00 CET 2006 /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh srcvol = mblok1+.feat/stats/*.img srcreg = mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 ERROR: analyzeRead(): cannot find any files for mblok1+.feat/stats/*.img ERROR: could not read mblok1+.feat/stats/*.img as type 16 ERROR: with mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh When I ran mri_vol2surf manually (see command line below; $out1 = the output dir I created manually to store the results in), the computer runs forever displaying a vol2surf_linear message. I left it running overnight and it didn't finish. Any suggestions in what I could alter to get it right? The functional overlay works fine with tkmedit. Thanks in advance, Niels van Strien mri_vol2surf --src $datalocation/mblok1+.feat/stats/zstat1.nii --srcreg $datalocation/mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out $out1/zstat1.nii.mgh --surf white --out_type mg srcvol = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/stats/zstat1.nii srcreg = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 WARNING: missing NIfTI-1 orientation (qform_code = 0) WARNING: your volume will probably be incorrectly oriented Done loading volume Reading surface /media/userdata/subjects/bert2/surf/lh.white INFO: NOT fixing vertex area Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 74277/126030 2 0 0 0 vol2surf_linear: nhits = 74277/126030 3 0 0 0 vol2surf_linear: nhits = 74277/126030 4 0 0 0 vol2surf_linear: nhits = 74277/126030 5 0 0 0 vol2surf_linear: nhits = 74277/126030 6 0 0 0 vol2surf_linear: nhits = 74277/126030 7 0 0 0 vol2surf_linear: nhits = 74277/126030 8 0 0 0

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Multiple warnings and errors in autorecon1
by Daniel Goldenholz 29 Jan '06

29 Jan '06

Hi Freesurfers, It has been a long time since I had the pleasure of recon-all'ing anything. Many things have changed. I ran recon-all today (based on the dev installation) and I got all sorts of interesting warnings. Should I care? If so, what should I do? Below are a few selected lines from the huge pile of output from autorecon1... ... $Id: fsl_rigid_register,v 1.13 2006/01/24 19:51:34 greve Exp $ Sun Jan 29 12:44:41 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00036 calling eval flirt -in /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-2.hdr -out /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-1.hdr -omat /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image ... mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2831/nu0.mnc Can't find the talairach xform '/autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm does not exist ... ... trying /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm ...which does not exist .... Iteration 1 Sun Jan 29 12:53:19 EST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.2831/nu0.mnc ./tmp.mri_nu_correct.mni.2831/nu1.mnc Not implemented yet in cache_volume_range_has_changed() Mode: atlas analysis ****VALIDATION*** THE SEGMENTATION IS PROBABLY NOT CORRECT .... -- Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon" "Life and death are in the hands of language" - Proverbs 18:21

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[Freesurfer] problem in autorecon1, checking the talairach transform
by Ryu-Ichiro Hashimoto 27 Jan '06

27 Jan '06

Dear all, I am trying "RecommendedReconstruction", following Wiki instruction. My problem is, after the first step of recon-all ("recon-all -autorecon1") when I try to check the talairach transform (by tkregister2 --mgz ... --fstal), I get an image incorrectly aligned ... image is displayed in quadrant (pls see ac_aft_reconall1_target.jpg). In this display, I cannot manually adjust it for coregistration. When I continue to run autorecon2, it crashes. For checking skull strip, it is correctly displayed (ac_aft_reconall1_tkmedit.jpg). I thought problem could be already present in converting from dicom to mgz, as there seems to be some missing info (message_conv.txt), though I am not sure whether it is really relevant. The image was obtained by 3T GE magnet with SPGR at BWH. Any thoughts regarding above are greatly appreciated. Thanks in advance for your help. Ryu Hashimoto mri_convert -it dicom -ot mgz 001/ 001.mgz reading from 001/... 256 DICOM 3.0 files in list Found 256 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 256. reading DICOM image... ------------------------------------------------- DICOM meta-header file name 001/dspgr_wa_001.dcm Date and time study date not found study time not found series time acquisition time Identification patient name not found manufacturer not found Dimensions number of rows 256 number of columns 256 number of frames 256 pixel width 0.94 pixel height 0.94 slice thickness 0.94 field of view 240.64 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time not found repetition time not found inversion time not found echo number not found flip angle not found bits allocated 16 Spatial information first image position 0 0 0 last image position 0 0 239.7 image orientation -1 0 0 0 -1 0 ------------------------------------------------- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (0, 0, 1) writing to 001.mgz...

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mri_mask bug
by Yuhong Jiang 27 Jan '06

27 Jan '06

Hi, We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on RedHat 9 and encountered a problem with the command mri_mask. It is not at all working. Here is what we entered as input: mri_mask input.mgz mask.mgz output.mgz No matter what we put as the mask, the input.mgz and output.mgz are always identical. Is there a bug with this command? (The command says "writing masked volume to output.mgz..." then about 10 seconds later it's done - although nothing is done). Thanks. --Yuhong ============================================================================= Yuhong Jiang yuhong(a)MIT.EDU 617-876-2054 http://web.mit.edu/yuhong/www =============================================================================

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label to mask
by Roger Alvaredo 27 Jan '06

27 Jan '06

Hello! I am a new user of Freesurfer. I have done the parcellation of a subject and it seems correctly. Now, I would like to know how to do this: 1. How could I assemble some labels in one and export this to a binary mask?? Thanks!

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making cutsom .tcl files
by Goldman, Aaron (NIH/NIMH) [C] 26 Jan '06

26 Jan '06

Hi, can someone recommend a good help or reference site for making tksurfer/tkmedit .tcl files? Thanks, -Aaron- Aaron L. Goldman Kelly Contractor Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

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nu_correct
by N.M. van Strien 26 Jan '06

26 Jan '06

Hi, I am having a problem with running the recon-all script. As soon as I get to intensity normalization, the script stops and gives an error for nu_correct (see output below). The MNI tools seem to be set up correctly however. The environment is set up as such that: MINC_BIN_DIR /usr/local/freesurfer/lib/mni/bin and this is where nu_correct does live. Any idea how to overcome this problem? I am running Fedora Core 3 and both the RH9 dev release as well as the CentOS4_x64 dev release show this problem. Thank you for your help, Niels van Strien Nu Intensity Correction Thu Jan 26 16:42:22 CET 2006 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=1000.00, 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 nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc nu_correct: Command not found. ERROR: nu_correct Linux VUMC 2.6.12-1.1381_FC3smp #1 SMP Fri Oct 21 04:22:48 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with errors at Thu Jan 26 16:42:30 CET 2006 Niels M. van Strien (MSc) Dept. of Anatomy Vrije Universiteit University Medical Center Room MF-G130 Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands tel: +31 20 44 48047 fax: + 31 84 222 7040 e-mail: n.vanstrien(a)vumc.nl http://anatomie.med.vu.nl/afdeling/persons/vanstrien.html

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4T data converting
by Du, Antao 25 Jan '06

25 Jan '06

Hi, I am trying convert the data from our 4T (Siemens) to mgz. But there is error message of "Floating exception": [antao@freesurfer fad131]$ mri_convert MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA ../FAD131/mri/orig mri_convert MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA ../FAD131/mri/orig reading from MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA... Floating exception [antao@freesurfer fad131]$ Can someone help me solve this problem? Thanks, Antao

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FW: [Freesurfer] overlay thickness maps
by Kirk, Gregory 23 Jan '06

23 Jan '06

-----Original Message----- From: Kirk, Gregory Sent: Monday, January 23, 2006 4:25 PM To: 'Kevin Teich' Subject: RE: [Freesurfer] overlay thickness maps Yes Kevin, im still a dum dum sometimes, as your comment I Looked it in shell window, and saw all was not well. In response to Load-Overlay-> load lh.thickness from the subject surf/ Directory get errors % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % mri_read(): couldn't determine type of file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness surfer: couldn't load /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness sclv_read_from_volume: error in MRIreadInfo. The overlays that are loaded in the buckner are .mgz files and it does not seem happy with these Doug Greve is the winner in our best suggestion category with Another method is to use mri_surf2surf to to convert the curv file into an mgh file (run it with --help to see how to use it). Then just load the mgh file as an overlay (with "compute identity"). Which when applied with- and the output is- [gkirk@Nuit surf]$ mri_surf2surf --hemi lh --srcsubject MASONO --srcsurfval thickness --src_type curv --trgsubject MASONO --trgsurfval lh.thickness.mgz --trg_type mgz srcsubject = MASONO srcval = thickness srctype = curv trgsubject = MASONO trgval = lh.thickness.mgz trgtype = mgz surfreg = sphere.reg hemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.sphere.reg Loading source data Reading curvature file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.thickness INFO: trgsubject = srcsubject Saving target data Reshaping 2 (nvertices = 107662) Gives .mgz files that surfer is happy to use as an overlay, and produces what looks like good Thickness maps. Thanks all Greg. -----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Friday, December 23, 2005 5:33 PM To: Kirk, Gregory Cc: Freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] overlay thickness maps There are a couple things that could be wrong. Make sure that calculating an identity registration is the proper thing to be doing here. Doug can probably tell you more about this. Next, is the file actually loading? Make sure that the output to the shell doesn't have any errors, and that there's a new line in the label/value area with the overlay's name on it. Make sure that there are actually values in that line as you move the mouse aroudn over the surface. If there are, do View->Configure->Overlay and see if you can set the threshold so that it encompasses the values, as the default threshold might be incorrect. On Fri, Dec 23, 2005 at 03:42:31PM -0500, Kirk, Gregory wrote: > > 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 -> $SUBJECTS_DIR/subject/surf choose > lh.thickness > * calculate identity map > > it redraws the surface but there is no colormap of the thickness -- Kevin Teich

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notes on Jan 2006 release
by Sasha Wolosin 23 Jan '06

23 Jan '06

Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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