Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

{Disarmed}
by hankee 23 Mar '07

23 Mar '07

hi,I have some question to ask.First,I use flash black and white checkboard as stimulate,blocked design which presents off(30second)-on(30s)-off(30s)-on(30s)-off(30s)-on(30s) pattern,so such stimulation lasts 3 minutes,TR=3s.In order to create the sem_assoc_s001_r100.dat file,I write the optseq command as bellow:optseq -ntp 60 -npercond 3 -tpercond 30 -o sem_assoc-s,I don't why whether is right or not? Besides that another command shows bellow:mkanalysis-sess -analysis sem_assoc -TR 3 -paradigm sem_assoc.par -designtype blocked -funcstem fmc -inorm -fwhm 4 -nconditions 1 -timewindow 30 -tprestim 31,I also do't know whether right or not? Second,the surf-sess command produce the surface,But the active area is very tiny,compare to the SUMA.the picture is in the attachment. how to adjust its colour and size? Thank you very much!!!

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Re: [Freesurfer] Complex value color scales.
by Kevin Teich 23 Mar '07

23 Mar '07

> I am trying to display phase information on the cortical surface using tksurfer, > but am running into problems with the scale bar. Specifically when plotting > scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice > looking (continulus) cortical maps, with the correct scale values, but the > color bar is showing up inconsistent (two colors). Is there any way to correct > this problem, or access the actual color values being projected to the cortical > mesh? Unfortunately, the scale bar isn't really meant to be used with the complex color wheel. There is no way to get a nice legend for the color wheel. However, if you select View->Information->Angle, you can see the actual value that is being passed into the color function, so you can mouseover a color on the surface and see what value is mapped to it. I know it's not great, but maybe it will help a bit. -- Kevin Teich

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Re: Freesurfer Digest, Vol 37, Issue 21
by Sebastian Moeller 23 Mar '07

23 Mar '07

Not being Roland and al... On 23. Mar 2007, at 18:49 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Thu, 22 Mar 2007 15:18:05 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 16 > To: Paul Aparicio <aparicio(a)mit.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.0703221517330.3420(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > no, definitely don't use COR. I think you can use mri_convert -i[ijk]s. > Rudolph: can you elaborate on how to do this? here is what I use to accomplish this (in a csh script): set targ_dir = /path/to/your/input_volumes set targ_file_name = example.mgz set conformed_vol = the_name_of_the_volume_with_faked_resolution.mgz mri_convert -i ${targ_dir}/${targ_file_name} -o ${targ_dir}/${conformed_vol} -iis 1 -ijs 1 -iks 1 CAVEAT this expects isometric input scans, otherwise it gets a bit more elaborate...: this is what I used in the days of non-isometric scanning. It will express all resolutions as multiples of the minmum so that resampling later (by running mri_convert -cm ...) will do something reasonable. You still have to make sure, that you have <= 256 voxels per dimension... ahoi & hope it helps Sebastian ##### silly script to follow...###### #! /bin/csh! # run number from the dicom file zero padded to three digits set run = 008 # number of the first dicom file to contain data for this run (actually any dicom file for a run should do'?) set first_dicom = 34840259 # the session to work on set session_dir = 050610Lupo set dicom_dir = 06131042 set user_id = moeller # where does the dicom data live set src_dir = /space/data/raw_data/20${session_dir}/ set src_file = $src_dir/$first_dicom # where to put the cor files set targ_base_dir = /space/data/${user_id}/cooked/anatomicals/$session_dir/mri mkdir $targ_base_dir # the next one has to match the run number from the dicom information... set targ_dir = $targ_base_dir/orig # get the dimensions (read from unpack.log) # let's do it like freesurfer does (no error checkin though) set first_two_dims = `mri_probedicom --i $src_file --t 28 30` # tag 28 30 is of form 0.453125\0.453125, so split the critter at the back slash #echo $first_two_dims set first_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\"); print a[1]}'` #echo $first_dim set second_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\"); print a[2]}'` #echo $second_dim # the slice resolution either in tag 18 50 or 18 88 set third_dim = `mri_probedicom --i $src_file --t 18 50` #echo $third_dim # get the shortest dimension, all this requires gnu bc to be installed set min_dim = `echo "min = $first_dim; if (min > $second_dim) { min = $second_dim }; if (min > $third_dim) { min = $third_dim }; min" | bc -l` set iis = `echo "scale=6; $first_dim / $min_dim" | bc -l` set ijs = `echo "scale=6; $second_dim / $min_dim" | bc -l` set iks = `echo "scale=6; $third_dim / $min_dim" | bc -l` #for unpacking at raw resolution mri_convert -i $src_file -o $targ_dir -it siemens_dicom -ot mgh #-iis $iis -ijs $ijs -iks $iks #end of script... ################################################### -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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maximum number of ROI in atlas
by Leila BH 23 Mar '07

23 Mar '07

Hello, I am modifying the 35-entries atlas by subdividing some parcels into N rois. Is there any limitation of the number of regions in an Atlas? Or an annotation file? Because when I have more than 300 region of interest in the atlas, the display of some region failed (gray) and the corresponding label became none. Do you know why? Leila

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Parts of tempral lobes not included
by deepa preeti 23 Mar '07

23 Mar '07

Hi Bruce: I appreciate if you could suggest how to intervene manually to fix this topology error - parts of superior & middle temporal regions not included in orig surface but included in brainmask & wm.mgz. Any suggestions is much appreciated. Thanks, Deepa. -- Deepa Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute 100 High St. Buffalo, NY 14203 Work: 716-859-7038 E-Mail: dramasamy(a)bnac.net

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FW: MINC Startup
by Alex Fornito 22 Mar '07

22 Mar '07

Hi, We've just installed version 3.05 for Mac and get the error below when running -autorecon1. I've noticed this error has been posted to the list a few times, but it always seems to have been resolved internally. Any help is much appreciated. Thanks, Alex Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/ darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level/Network/Library /Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6/Library/Perl/5.8.1.) at /usr/ local/freesurfer/lib/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/lib/mni/bin/nu_correc t line 37. ERROR: nu_correct

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parts of temporal lobe not included
by deepa preeti 22 Mar '07

22 Mar '07

Hi Bruce: I looked at the brainmask.mgz and wm.mgz - obviously the pial is not included in superior & middle temporal regions in the brainmask.mgz and in the wm.mgz. The wm intensities are ranging from 96 - 106 in the missing superior & middle temporal regions in the brainmask.mgz. I have attached the brainmask.mgz, wm.mgz, aseg.mgz & aseg+aparc.mgz, all with pial, white and orig surfaces overlaid. As mentioned earlier, I had control points added in wm of excluded temporal regions and ran this command again ( to fix pial surface ) : recon-all -autorecon2-cp -autorecon3 -subjid subject The final image did not include the excluded temporal region after opening up in: tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white But gave me different values for entire regions in lh & rh aparc and aparc.a2005.stats - cov >1% in all regions. For example, Before adding control point After adding control point COV lh superior temporal(mm2) 3487 3102 8.3% rh superior temporal (mm2) 3434 3370 4.9% lh middle temporal(mm2) 3902 3001 18.5% rh middle temporal (mm2) 3046 3528 10.4% Another question: if you run this command > recon-all -autorecon2-cp -autorecon3 -subjid subject < Do we run the entire subcortical segmentation as well? I appreciate your suggestions. Deepa. Deepa Preeti Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute Department of Neurology Buffalo General Hospital 100 High St. Buffalo, NY 14203 Work: 716-859-7038 E-Mail: dramasamy(a)bnac.net

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Re: Freesurfer Digest, Vol 37, Issue 16
by Paul Aparicio 22 Mar '07

22 Mar '07

Hi Bruce, regarding the high res recon, you mention that you can change the info w/o changing the data using mri_convert, and this should keep mri_normalize from conforming the data to 1mm voxels? Do you know the commands that accomplish this? I have tried changing the file to COR format and editing the file to do as you suggest, the change it back to mgz, but mri_normlaize still conforms the volume to 1mm? Thanks Paul On Tue, 20 Mar 2007 freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." >

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intergroup t-values
by Cameron Ellis 22 Mar '07

22 Mar '07

Hi all, I am trying to generate a t-map for an intergroup average. when I attempt to run stxgrinder the program looks for a fixed effects average. Since intergroupavg-sess assumes a random effects analysis is it possible to generate this statistic? Is there something statistically repugnant about generating a t-statistic for an intergroup random effects average? Thanks, Cameron

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gray matter misclassified as csf
by Binyam Nardos 21 Mar '07

21 Mar '07

Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

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