Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

White matter separation problem
by Juergen Haenggi 14 May '08

14 May '08

Dear FS experts We run FS on several subjects one of whom had an technical artefact on the MR image that seems to prevent adequate white matter extraction (see attachment). Beside the exclusion of this subject from the study local manual editing could be an opportunity. Is there another way to avoid the incomplete extraction of white matter such as increasing or decreasing the intensity value of white matter. What do you recommend? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Dimensions of an mgh file generated by mris_preproc
by Lars M. Rimol 13 May '08

13 May '08

Hi, I'm wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Why? Thank you! -- yours, LMR

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Re: ffx bug
by Doug Greve 13 May '08

13 May '08

Sorry, It's not "live" yet -- meaning that the stable version has not been updated yet. Usually, this happens overnight. You can tell by running: ls -l $FREESURFER_HOME/fsfast/toolbox/fast_selxavg.m doug xiaomin wrote: > Hi Doug, > > > > The significance of ffx with percent is still very small from -0.0249 > to 0.0682, which is similar to what I got before. I am using stable 4. > > > > Xiaomin > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, May 13, 2008 5:32 PM > To: xiaomin > Cc: 'Roger Tootell'; 'Daphne Holt'; 'Brittany Cassidy'; 'Free Surfer' > Subject: Re: ffx bug > > > > There were a bunch of voxels with no significance because the ffx > noise had essentially been multiplied by 100 (so 100 times more noise > than there really was). make sense? > > xiaomin wrote: > > Hi Doug, > > > > Thanks for fixing it. I will rerun the group analysis and let you > know if it works. However, it is still puzzling to me why the > significant histogram from the ffx without percent (as attached in my > last email) looks so weird. The maximum is too large. Also, the > shape of the significant ffx histogram should not be different for > percent vs. non-percent. > > > > Xiaomin > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, May 13, 2008 5:13 PM > To: xiaomin > Cc: analysis-bugs(a)nmr.mgh.harvard.edu > <mailto:analysis-bugs@nmr.mgh.harvard.edu>; 'Roger Tootell'; 'Daphne > Holt'; 'Brittany Cassidy'; Free Surfer > Subject: Re: ffx bug > > > > > Hi Xiaomin, I finally got around to looking at this, and this is a > bug. The "cespct" is not actually a percent, rather it is a fraction > of the mean functional. However, the "cesvarpct" is a percent, which > makes the group ffx analysis with percent fail. I have fixed this in > both dev and stable such that cespct is actually a percent, live on > next update. Let me know if this does not fix your problem. > > doug > > > > > xiaomin wrote: > >Hi, > > > >I am running the following command for group fixed factor and random factor > >analysis with and without percent parameter on. > > > >Here are the commands: > >1) for the no percent: > >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats > >-hemis -o . -subject fsaverage > >mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask > >../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf > >fsaverage rh > > > >2) for the percent: > >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats > >-percent -hemis -o . -subject fsaverage > >mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask > >../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf > >fsaverage rh > > > >However, the significance between percent and no percent is inconsistent. > >For testing if the data has problem, I run it with rfx design. The > >significance between percent and no percent is almost same. (see attached > >graph) Second, the significance with percent parameter for the fixed factor > >analysis is very small, which is abnormal. We need to use ffx significant > >map to define a ROI. > > > >The data is here: > > > >/autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D > >epth. > > > > > >Xiaomin Yue > >Research Fellow > >NMR center, MGH > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > >-- > >Douglas N. Greve, Ph.D. > >MGH-NMR Center > >greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >Phone Number: 617-724-2358 > >Fax: 617-726-7422 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > >-- > >Douglas N. Greve, Ph.D. > >MGH-NMR Center > >greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >Phone Number: 617-724-2358 > >Fax: 617-726-7422 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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using func2sph-sess w/ FS4
by Susan Mosher 13 May '08

13 May '08

Hello all, I am trying to run func2sph-sess with FreeSurfer 4. When mri_vol2surf tries to run, it looks for a file called h_000.hdr. The version of selxavg I used produced h.nii, but not h_000.hdr. mri_vol2surf won't run without this file (h_000.hdr), and I am not sure how to specify that the needed file is h.nii (if this is, in fact, correct). Is there a way to specify that h.nii should be used? Thank you, ~Sue * * ** *** ***** ******** ************* Susan M. Mosher Program in Neuroscience Boston University office phone: 857-364-2214 smosher(a)bu.edu * * ** *** ***** ******** *************

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converting fieldsign files into volume space
by Kai Hwang 13 May '08

13 May '08

Hello Freesurfers, I recently used sfa-sess and paint-sess to analyze some retinotopy data, so far every works great. I wonder if there is a way to convert fieldsign overlays from surface space into volume space? I tried mri_surf2vol but it doesn't seem to recognize that file format: hwang@kaih:~/Subjects/FSFAST/VM_1/bold/VM0/fieldsign> mri_surf2vol --surfval ./fieldsign --hemi lh --volreg ~/Subjects/FSFAST/VM_1/bold/register.dat gdiagno = -1 ERROR: cannot recognize the type of ./fieldsign any suggestions how to make this work? Also could someone explain to me whats the difference between fieldsign-lh fieldsign-lh.mgz fieldsignmask-lh fieldsignmask-lh.mgz what is the difference of having a mgz or mask extension? Thank you! Kai

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difference maps
by Elif SIKOGLU 13 May '08

13 May '08

Hello, We are using mri-surfcluster to output ocn files. The default format seems to be volume encoded surface file which seems to be a long array and it is unreadable by MRIread. Is there a way to convert this file into something that is readable by Matlab? Alternately, we want to compare activations from sessions for different conditions for an individual subject. (We only have pilot data on two subjects and trying to form difference maps) Any recommendations? Thanks,

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Question: can't display retinotopy fieldsign data
by Kai Hwang 13 May '08

13 May '08

Hello, I'm trying to use freesurfer to map the visual cortex and get region borders of V1, V2.. etc. We used a conventional rotating/expanding wedge paradigm, and I followed the steps described in FsFastIndividualRetinotopy Analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis> Everything worked fine till the last step, I can't view the results with surf-sess. After I execute the command surf-sess, first a flatten cortex appeared, then the view screen turned black and nothing showed up. Here is what I have in the terminal window hwang@kaih:~/Subjects> surf-sess -s Pilot1 -a VM_retinotopy -retinotopy fieldsign -flat grep: /home/hwang/Subjects/Pilot1/session.info: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /home/hwang/Subjects/log/surf-sess.VM_retinotopy.fs.log ----------------------------------------------------------------- ------------------------------------------------------ ------------------------------------------------------ Session: Pilot1 ---- ------ lh hemisphere ------ /home/hwang/Subjects/Pilot1/bold/VM_retinotopy ---------------------------------------------------------- /home/hwang/Subjects/Pilot1/bold/VM_retinotopy tksurfer -Pilot1 lh inflated -tcl /usr/local/freesurfer/lib/tcl/fs-flat.tcl ---------------------------------------------------------- Loading /usr/local/freesurfer/surface_labels.txt surfer: current subjects dir: /home/hwang/Subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/hwang/Subjects/Pilot1/bold/VM_retinotopy surfer: Reading header info from /home/hwang/Subjects/Pilot1/mri/T1.mgz surfer: vertices=149915, faces=299826 can't find talairach file '/home/hwang/Subjects/Pilot1/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: ### redraw failed: no gl window open Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... tksurfer: fs-flat.tcl: set flags setdefpatchview: ### position.tcl for Pilot1 does not exist setdefpatchview: ### setting flatzrot to 90 (default) setdefpatchview: ### setting flatscale to 1.0 (default) setdefpatchview: ### setting flatxtrans to 0.0 (default) setdefpatchview: ### setting flatytrans to 0.0 (default) readenv.tcl: ==> read global setenv vars readenv: set invphaseflag 0 readenv: set fm fieldsign/fieldsignmask-lh readenv: set angle_offset 0 readenv: set dir /home/hwang/Subjects/Pilot1/bold/VM_retinotopy readenv: set truncphaseflag 0 readenv: set offset 0.4 readenv: set fmid 0.8 readenv: set fs fieldsign/fieldsign-lh readenv: set lat readenv: set fthresh 0.4 readenv: set complexname -imag readenv: set realname -real readenv: set eccendir eccen readenv: set floatstem map readenv: set hemi lh readenv: set rgbname map readenv: set use_vertex_arrays 0 readenv: set nosave 0 readenv: set polardir polar readenv: set noexit readenv: set curv lh.curv readenv: set patchname occip.patch.flat readenv: set fslope 1.3 readenv: set colscale 0 readenv: set mc () { . /usr/share/mc/bin/mc-wrapper.sh } readenv: set smoothsteps 2 readenv: set revpolarflag 0 readenv.tcl: ==> read rgbname-specific setenv vars % tksurfer: fs-flat.tcl: read curvature surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: /usr/local/freesurfer/lib/tcl/fs-flat.tcl surfer: curvature read: min=-1.677210 max=1.267429 % tksurfer: fs-flat.tcl: read patch tksurfer: fs-flat.tcl: read fieldsign tksurfer: fs-flat.tcl: read fieldsign mask surfer: read_fieldsign(fieldsign/fieldsign-lh) surfer: mris->nvertices = 149915, vnum = 149915 surfer: read_fsmask(fieldsign/fieldsignmask-lh) % tksurfer: fs-flat.tcl: scale, position brain surfer: ### GL window already open: can't open second % tksurfer: fs-flat.tcl: save rgb's tksurfer: fs-flat.tcl: save rgb surfer: dipscale=0.000000 % tksurfer: fs-flat.tcl: nosave setenv'd => nothing will be saved invalid command name "dontsave_rgb_named"% surfer: dipscale=0.000000 % surfer: dipscale=0.000000 any suggestion how to make surf-sess work? Thanks! Kai

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Re: ffx bug
by Doug Greve 13 May '08

13 May '08

There were a bunch of voxels with no significance because the ffx noise had essentially been multiplied by 100 (so 100 times more noise than there really was). make sense? xiaomin wrote: > Hi Doug, > > > > Thanks for fixing it. I will rerun the group analysis and let you > know if it works. However, it is still puzzling to me why the > significant histogram from the ffx without percent (as attached in my > last email) looks so weird. The maximum is too large. Also, the > shape of the significant ffx histogram should not be different for > percent vs. non-percent. > > > > Xiaomin > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, May 13, 2008 5:13 PM > To: xiaomin > Cc: analysis-bugs(a)nmr.mgh.harvard.edu; 'Roger Tootell'; 'Daphne Holt'; > 'Brittany Cassidy'; Free Surfer > Subject: Re: ffx bug > > > > > Hi Xiaomin, I finally got around to looking at this, and this is a > bug. The "cespct" is not actually a percent, rather it is a fraction > of the mean functional. However, the "cesvarpct" is a percent, which > makes the group ffx analysis with percent fail. I have fixed this in > both dev and stable such that cespct is actually a percent, live on > next update. Let me know if this does not fix your problem. > > doug > > > > > xiaomin wrote: > >Hi, > > > >I am running the following command for group fixed factor and random factor > >analysis with and without percent parameter on. > > > >Here are the commands: > >1) for the no percent: > >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats > >-hemis -o . -subject fsaverage > >mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask > >../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf > >fsaverage rh > > > >2) for the percent: > >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats > >-percent -hemis -o . -subject fsaverage > >mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask > >../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf > >fsaverage rh > > > >However, the significance between percent and no percent is inconsistent. > >For testing if the data has problem, I run it with rfx design. The > >significance between percent and no percent is almost same. (see attached > >graph) Second, the significance with percent parameter for the fixed factor > >analysis is very small, which is abnormal. We need to use ffx significant > >map to define a ROI. > > > >The data is here: > > > >/autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D > >epth. > > > > > >Xiaomin Yue > >Research Fellow > >NMR center, MGH > > > > > > > > > > ------------------------------------------------------------------------ > > > > > >-- > >Douglas N. Greve, Ph.D. > >MGH-NMR Center > >greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >Phone Number: 617-724-2358 > >Fax: 617-726-7422 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

Re: ffx bug
by Doug Greve 13 May '08

13 May '08

Hi Xiaomin, I finally got around to looking at this, and this is a bug. The "cespct" is not actually a percent, rather it is a fraction of the mean functional. However, the "cesvarpct" is a percent, which makes the group ffx analysis with percent fail. I have fixed this in both dev and stable such that cespct is actually a percent, live on next update. Let me know if this does not fix your problem. doug xiaomin wrote: >Hi, > >I am running the following command for group fixed factor and random factor >analysis with and without percent parameter on. > >Here are the commands: >1) for the no percent: >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats >-hemis -o . -subject fsaverage >mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask >../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf >fsaverage rh > >2) for the percent: >isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats >-percent -hemis -o . -subject fsaverage >mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask >../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf >fsaverage rh > >However, the significance between percent and no percent is inconsistent. >For testing if the data has problem, I run it with rfx design. The >significance between percent and no percent is almost same. (see attached >graph) Second, the significance with percent parameter for the fixed factor >analysis is very small, which is abnormal. We need to use ffx significant >map to define a ROI. > >The data is here: > >/autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D >epth. > > >Xiaomin Yue >Research Fellow >NMR center, MGH > > > > > > ------------------------------------------------------------------------ > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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imensions of an mgh file generated by
by Lars M. Rimol 13 May '08

13 May '08

Hi, I'm just wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Thank you! -- yours, LMR

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Freesurfer May 2008