Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Time
by Valtina Pouegue 07 Mar '13

07 Mar '13

Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the conversion to .mgz with the command recon-all -i <path-to-first-structural> [-i <path-to-second-structural>] -s <subjid> . All my folders are created but in the Orig folder I don't fige files .mgz. I think that the processing time is really long but I'm not sure. Do you know somthing about? Thanks. VP

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Viewing volumes and surfaces in Native Space
by Timothy Brown 07 Mar '13

07 Mar '13

Dear FreeSurfer users, I wish to view volumes and surfaces in native space. I used the information at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to convert volumes. I then used: tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6 When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached) Can you let me know the steps/procedure to do this? Many thanks, -Tim Timothy Brown email: timothy(a)cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218

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p[All] post-doc position available (fwd)
by Bruce Fischl 07 Mar '13

07 Mar '13

FYI ---------- Forwarded message ---------- Date: Thu, 7 Mar 2013 11:27:02 -0500 From: Dara Manoach <dara(a)nmr.mgh.harvard.edu> To: all(a)nmr.mgh.harvard.edu Subject: [All] post-doc position available Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA Project: Multimodal neuroimaging studies of sleep and memory PI: Dara S. Manoach, Ph.D. The position will involve investigating the role of sleep in memory consolidation, how these processes go awry in schizophrenia and autism, and the efficacy of pharmacological and other interventions. Our work has linked a specific cognitive deficit in schizophrenia (the reduction of sleep-dependent memory consolidation) to a particular mechanism (sleep spindles) and we have preliminary evidence of an effective intervention. In collaboration with Dr. Robert Stickgold?s lab at Beth Israel Deaconess Medical Center, we are extending and expanding this basic and clinical research program using state-of-the art tools including high density EEG (polysomnography), MEG, functional connectivity MRI, fMRI, and behavioral studies. We are seeking someone to participate in these NIMH-funded investigations who is familiar with MEG/EEG methodology and data analysis, comfortable with methodological innovation, and an interested in optimizing and developing analysis streams tailored to the study aims and populations. New approaches and ideas are encouraged, as are independent projects that dovetail with current studies. The position requires working closely with the PI, as well as with Dr. Stickgold, other Martinos Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG Core Lab, and lab mates to design studies, acquire data, and develop, explore, improve and apply data analytic techniques. Training in clinical research and in the acquisition, analysis, and interpretation of neuroimaging data will be provided. Requirements: PhD, Experience with MEG/EEG data analysis/methodology and/or other signal processing. Background in cognitive neuroscience, experimental psychology, and an interest in clinical applications are a plus. Position available immediately. Interested applicants should email: (a) CV, (b) statement of post-doctoral and career goals, (c) writing sample (e.g., a published manuscript), and (d) letters and/or contact information for three references to Dara Manoach at dara(a)nmr.mgh.harvard.edu. Stipend levels are in line with NIMH. A two-year commitment is required. Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 1.111 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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optimizing output
by Linn Mittlestein 07 Mar '13

07 Mar '13

Dear list, I was wondering whether you have any suggestions on how to optimize accuracy of the Freesurfer output (both cortical and subcortical) in images aquired on lower scanning resolutions than 3 T (for examle 1 T)? Kind Regards, Linn

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preproc-sess didn't work
by 古木 07 Mar '13

07 Mar '13

Hi,Doug When I run"preproc-sess -fsd bold -fwhm 0 -surface self lhrh -sf sessid -per-run",I met the following problems.Can you tell me why? preproc-sess sess01 $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ Linux localhost.localdomain 2.6.18-308.el5PAE #1 SMP Tue Feb 21 20:46:05 EST 2012 i686 i686 i386 GNU/Linux 2013年 03月 07日星期四 16:24:05 CST /usr/local/freesurfer/Project -fsd bold -fwhm 0 -surface self lhrh -sf sessid -per-run ProjectDir /usr/local/freesurfer/Project sess01 Template ----------------------------- mktemplate-sess -s sess01 -d /usr/local/freesurfer/Project -fsd bold -update Session: /usr/local/freesurfer/Project/sess01 ---------------- 2013年 03月 07日星期四 16:24:05 CST Detected input format at nii /usr/local/freesurfer/Project mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii /usr/local/freesurfer/Project/sess01/bold/template.nii.gz --frame 0 mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii /usr/local/freesurfer/Project/sess01/bold/template.nii.gz --frame 0 INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/Project/sess01/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999281, -0.0191918, -0.032696) j_ras = (-0.0194077, 0.999792, 0.00629985) k_ras = (-0.0325683, -0.00692988, 0.999445) keeping frame 0 writing to /usr/local/freesurfer/Project/sess01/bold/template.nii.gz... Run: 001 ---------------- 2013年 03月 07日星期四 16:24:08 CST /usr/local/freesurfer/Project mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii /usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz --mid-frame mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii /usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz --mid-frame INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/Project/sess01/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999281, -0.0191918, -0.032696) j_ras = (-0.0194077, 0.999792, 0.00629985) k_ras = (-0.0325683, -0.00692988, 0.999445) keeping frame 122 writing to /usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz... 2013年 03月 07日星期四 16:24:11 CST mktemplate-sess completed sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d /usr/local/freesurfer/Project -update ------------------------------------------------ /usr/local/freesurfer/Project/sess01 2013年 03月 07日星期四 16:24:11 CST mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_21890 /usr/local/freesurfer/Project/sess01/bold mri_convert template.nii.gz /tmp/mkbrainmask_21890/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_21890/in.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999281, -0.0191918, -0.032696) j_ras = (-0.0194077, 0.999792, 0.00629985) k_ras = (-0.0325683, -0.00692988, 0.999445) writing to /tmp/mkbrainmask_21890/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/Project/sess01/bold bet.fsl /tmp/mkbrainmask_21890/in.nii /tmp/mkbrainmask_21890/brain -m -f 0.1 /usr/local/freesurfer/bin/bet.fsl: line 150: /bin/remove_ext: 没有那个文件或目录 /usr/local/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: 没有那个文件或目录 /usr/local/freesurfer/bin/bet.fsl: line 153: /bin/imtest: 没有那个文件或目录 /usr/local/freesurfer/bin/bet.fsl: line 153: [: =: unary operator expected /usr/local/freesurfer/bin/bet.fsl: line 231: /bin/bet2: 没有那个文件或目录 mri_binarize --i /tmp/mkbrainmask_21890/brain_mask.nii --min .01 --o /tmp/mkbrainmask_21890/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_21890/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/Project/sess01/bold cmdline mri_binarize --i /tmp/mkbrainmask_21890/brain_mask.nii --min .01 --o /tmp/mkbrainmask_21890/brain_mask.nii sysname Linux hostname localhost.localdomain machine i686 user root input /tmp/mkbrainmask_21890/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_21890/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 If I want to run preproc-sess,do I have to install FSL? Why I can't use the mkanalysis -gui ? Thanks LiuYong

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Re: [Freesurfer] Error
by Shantanu Ghosh 07 Mar '13

07 Mar '13

Hi Chikku-- What is your discrete variable? does it have more than one level? is it entered in the fsgd file? It looks like your discrete variable(s) is not defined properly. It must have at least two levels (e.g. Male/Female, RightHanded/LeftHanded, etc.). Check your fsgd file to so it is properly constructed: check the following link for formatting a legal fsgd file. http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat shantanu On Thu, March 7, 2013 7:40 am, Varghese Chikku wrote: > shantanu, > Many Thanks > Still error loading data, > this is what i am getting. > - freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > chikkus-MacBook-Pro:~ chikkuvarghese$ cat > /Users/chikkuvarghese/subject/qdec/anatomy.levels > right hippocampus > left hippocampuschikkus-MacBook-Pro:~ chikkuvarghese$ qdec > > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > > Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... > Number of columns: 4 > fsid column: 1 > Number of factors: 3 > Number of subjects: 2 > Reading discrete factor levels from config file > /Users/chikkuvarghese/subject/qdec/age.levels > age > 70 > 71 > done. > Reading discrete factor levels from config file > /Users/chikkuvarghese/subject/qdec/anatomy.levels > right hippocampus > done. > ERROR: /Users/chikkuvarghese/subject/qdec/anatomy.levels is invalid. Must > have at least two levels. > Error loading the data table. > > > Kind Regards > chikku > > > > > > > > > > On 6 March 2013 18:19, Shantanu Ghosh <shantanu(a)nmr.mgh.harvard.edu> > wrote: > >> ok try editing qdec.table.dat by just pressing <Enter> after the subject >> with the error and the last line >> hth. shantanu >> >> On Wed, March 6, 2013 12:12 pm, Varghese Chikku wrote: >> > no luck Shantanu >> > This comes up >> > Loading data table >> /Users/chikkuvarghese/subject/qdec/qdec.table.dat... >> > Number of columns: 4 >> > fsid column: 1 >> > Number of factors: 3 >> > Number of subjects: 1 >> > ERROR: QdecDataTable::Load: problem parsing file >> > /Users/chikkuvarghese/subject/qdec/qdec.table.dat >> > This line did not appear to end with a newline: >> > truetest2.long.ie 70 m >> lefthippocampus >> > Error loading the data table. >> > >> > this is what i did xedit qdec.table.dat/ and saved in to the qdec >> > directory.After i saved it I noticed this,and extra file >> > saying qdec.table.dat.textClipping >> > Am I doing something terribly wrong, >> > Sorry >> > chikku >> > >> > On 6 March 2013 17:34, Shantanu Ghosh <shantanu(a)nmr.mgh.harvard.edu> >> > wrote: >> > >> >> Hi Chikku-- can you try with a /newline at the end of your .dat file? >> >> shantanu >> >> >> >> On Wed, March 6, 2013 10:40 am, Varghese Chikku wrote: >> >> > All, >> >> > Any idea how can I sort this error, >> >> > Loading data table >> >> /Users/chikkuvarghese/subject/qdec/qdec.table.dat... >> >> > Number of columns: 4 >> >> > fsid column: 1 >> >> > Number of factors: 3 >> >> > Number of subjects: 1 >> >> > ERROR: QdecDataTable::Load: problem parsing file >> >> > /Users/chikkuvarghese/subject/qdec/qdec.table.dat >> >> > This line did not appear to end with a newline: >> >> > truetest2.long.e Female 70 >> >> > Righthippocampus 4006 >> >> > Error loading the data table. >> >> > >> >> > Many Thanks >> >> > chikku >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer(a)nmr.mgh.harvard.edu >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> -- >> >> Shantanu Ghosh, Ph.D. >> >> Harvard Medical School & Massachusetts General Hospital >> >> Martinos Center for Biomedical Imaging >> >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to >> whom >> >> it >> >> is >> >> addressed. If you believe this e-mail was sent to you in error and >> the >> >> e-mail >> >> contains patient information, please contact the Partners Compliance >> >> HelpLine at >> >> http://www.partners.org/complianceline . If the e-mail was sent to >> you >> >> in >> >> error >> >> but does not contain patient information, please contact the sender >> and >> >> properly >> >> dispose of the e-mail. >> >> >> >> >> >> >> > >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> >> >> > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

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FS workshop registration link
by Nooshin Zadeh 07 Mar '13

07 Mar '13

Dear All I have a question about upcoming Freesurfer course registration (April 29 _ May 1). The registration link was supposed to be open and sent by today, but I still have not received it. I was wondering if you have any information and can help me. Thanks a lot Nooshin

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Advice on integrating FSL's BET with recon-all
by Winter, Warren 06 Mar '13

06 Mar '13

Hi again, We have had some suboptimal results from FreeSurfer's skullstripping algorithm, even after iteratively trying different watershed thresholds and after checking the quality of Talairach registration. The results are pretty good, but often leave some dura matter and bits of neck behind whose higher intensity values, I believe, may end up skewing recon-all's later estimation of the range of intensity values within grey matter, and consequently compromising the accuracy of pial surface estimation. FSL's BET, however, seems to do a better job of extracting the brain, at least for our dataset. So, I was wondering if I might be able to skip over mri_watershed and feed autorecon2 and autorecon3 a brainmask.mgz file created using BET. I tried this procedure: 1) mri_convert <path/to/T1dcm> T1.nii.gz 2) bet T1.nii.gz BET_brainmask.nii.gz -A 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz 4) recon-all -s <subjid> -autorecon1 -noskullstrip 5) mv BET_brainmask.nii.gz ./<subjid>/mri/brainmask.mgz 6) recon-all -s <subjid> -autorecon2 -autorecon3 And I got this error message, right after normalization2: " #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_bet/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 " I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match those of brainmask.mgz, resulting during normalization2 in a mismatch between brain.mgz and brainmask.mgz. Does that seem right, and is there a possible workaround? Thank you! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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Cannot see control points in tkmedit and freeview when connecting through X11
by Caspar M. Schwiedrzik 06 Mar '13

06 Mar '13

Dear Freesurfer Team, when I am trying to set control points in tkmedit (FS 5.1 or 4.5) or to see control points in Freeview (FS 5.1), I run into a strange problem when I connect to our server through X11. Namely, I cannot see the control points, although they are being set when I place them (they are saved in the respective .dat file). When I switch to a mosaic view, I can sometimes briefly see them, but as soon as I try to place new ones, the old ones disappear again. Any known workaround (apart from using VNC)? Thank you very much, Caspar

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preproc-sess
by Meryem Ayse Yucel 06 Mar '13

06 Mar '13

Hi all, I am running: preproc-sess -s sess01 -fsd bold -fwhm 5 -stc up -per-run However at the end it did not create an output like fmcsm. I only have fmc.nii, fmc.up.nii and fmcpr.up.nii. Am I doing something wrong, or these outputs are smoothed too? Thanks, Meryem

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Freesurfer March 2013