Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

mri_cc / aseg issue.
by Jamie Hanson 07 May '09

07 May '09

Hi Freesurfer folks- I created a custom aseg atlas and now, I am running into some issues w/ recon-all. Here is part of my terminal output... --- cp aseg.auto.mgz aseg.mgz #-------------------------------------- #@# CC Seg Wed May 6 20:40:19 CDT 2009 mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz 162_aseg reading input aseg from aseg.auto.mgz writing aseg with cc labels to aseg.auto_CCseg.mgz mri_cc: volume /study/eemri/data/proc/freesurfer/162_aseg/mri/aseg.auto.mgz already has CC in it reading aseg from /study/eemri/data/proc/freesurfer/162_aseg/mri/aseg.auto.mgz Linux pasilla.keck.waisman.wisc.edu 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 07:03:59 EDT 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 6 20:40:22 CDT 2009 ------ Thoughts? Did my aseg creation go awry? Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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Help with skull strip
by Drosos, Athena 07 May '09

07 May '09

Hi, I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing. Thank you, I look forward to hearing your response. Sincerely, Athena

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ERROR: could not read header info from T1 or orig
by anita di iasio 07 May '09

07 May '09

Hi, I have a problem: In the past Freesurfer runs and all go right. Now when I run tksurfer command, a error message appears: surfer: current subjects dir: models/buckner_data/tutorial_ subjs/group_analysis_tutorial/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/anita/models/buckner_data/tutorial_subjs/group_analysis_tutorial ERROR: could not read header info from T1 or orig in models/buckner_data/tutorial_subjs/group_analysis_tutorial//004/mri It is strange because the error message appears with tutorial data. Can anybody help me? Thanks, Anita

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Re: [Freesurfer] Problem with space in directory or file name
by Ed Gronenschild 07 May '09

07 May '09

Hi Sita, That doesn't work. I have to write a script to remove the space. ed On 7 May 2009, at 1:15, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Hi Ed, > > You can try inserting a backslash and then a space in the filename. > eg.. if you have 'dicom file.dcm', you might want > to try > > recon-all -all -i dicom\ file.dcm -s ............. > > > Sita. > > > > > On Wed, 6 May 2009, Ed Gronenschild wrote: > >> Hi, >> >> Whenever I want to convert DICOM files to .mgz file I have to >> remove spaces in the directory name or file names otherwise >> recon-all -i ... -s ... will not work. >> Bracketing the names within quotes will not help. >> Is there some workaround? >> >> ed >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Problem with space in directory or file name
by Ed Gronenschild 06 May '09

06 May '09

Hi, Whenever I want to convert DICOM files to .mgz file I have to remove spaces in the directory name or file names otherwise recon-all -i ... -s ... will not work. Bracketing the names within quotes will not help. Is there some workaround? ed

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problem downloading freesurfer
by Dana W. Moore 05 May '09

05 May '09

I am trying to download FreeSurfer onto a different Linux machine. I am able to download, but when I try to unzip the files, I get this error message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I have tried downloading it repeatedly with the same outcome. Do you know what the problem might be? I am downloading the <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer-Linux…>freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz file. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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fMRI FOV issue (Bay 8)
by Dave Brohawn 05 May '09

05 May '09

Hello, My bugr info is at the bottom, if needed: I was doing a recon-all on one of our subjects, and I received this error message: **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** I pasted this error message into the archives, and saw Nick had asked someone with a similar problem to check the FOV of their subject to see if it was greater than 256 via mri_info orig.mgz. Our subject, FB0011055B, has an FOV of 320, and dimensions 320 X 320 X 320. This is unusual because we opened the same set protocol as we usually do and did not make any adjustments to the FOV or slice parameters. Most of our subject's orig.mgz info looks like this - Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.7146 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 24.6542 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.7758 talairach xfm : /autofs/space/seymour_001/users/folate_subjects/FB0011053B/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.2854 0.0000 0.0000 1.0000 -103.3458 0.0000 -1.0000 0.0000 101.2242 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.2854 -0.0000 -0.0000 -1.0000 101.2242 -0.0000 1.0000 -0.0000 103.3458 0.0000 0.0000 0.0000 1.0000 This subject's is different, and it looks like this: Volume information for orig.mgz type: MGH dimensions: 320 x 320 x 320 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 320.000 dof: 0 xstart: -160.0, xend: 160.0 ystart: -160.0, yend: 160.0 zstart: -160.0, zend: 160.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.2500 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 158.7500 0.0000 0.0000 1.0000 -160.0000 0.0000 -1.0000 0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 158.7500 -0.0000 -0.0000 -1.0000 160.0000 -0.0000 1.0000 -0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 Any ideas as to why this would happen? Also, what does this -cw256 flag do and will it fix the issue? **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** Thank you, Dave Brohawn FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090503 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects cd /space/seymour/1/users/folate_subjects

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mris_preproc really averages?
by Jeff Sadino 04 May '09

04 May '09

Hello, I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Rediscover Hotmail®: Get quick friend updates right in your inbox. http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Up…

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Analysis without and with a covariate
by Jürgen Hänggi 04 May '09

04 May '09

Dear FS experts I have done an analysis without a covariate. Now, I want to do the same analysis but including mean cortical thickness as a covariate. I am wondering whether I have to run all steps again incl. mris_preproc or whether it is sufficient to only run mri_glmfit with the new FSGD file that includes the covariate. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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recon-all w/ custom aseg atlas.
by Jamie Hanson 04 May '09

04 May '09

Hi Freesurfer folks- So I have been trying to create a custom aseg atlas (which I did, thanks much to Bruce and Nick!)... Now I want to run recon-all w/ that new custom aseg atlas (on additional subjects not included in .gca / atlas creation)... I checked the web and the listserv archive, but might have missed it... Is there an easy way to simple specify this new aseg atlas to run w/ recon-all? Or do I just need to run each command for autorecon1 and autorecon2 and just replace the default .gca file when I run mri_em_register, mri_watershed, mri_ca_normalize, mri_ca_register, mri_remove_neck, and mri_ca_label? Thanks much! jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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