Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

Re: [Freesurfer] Total GM and WM volumes
by Ed Gronenschild 04 Nov '10

04 Nov '10

Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 - 251139 = 281628 gm rh = 536127 - 254730 = 281397 Left + right: total = 1068894 wm = 505869 gm = 563025 ------------ The aseg.stats file lists the following results: cortical wm lh: 251139 cortical wm rh: 254730 total wm: 505869 cortical gm lh: 263888 cortical gm rh: 265231 total cortical gm: 529119 subcortical gm: 181270 total gm: 710389 -------------- For wm both results are equal but for gm they are not. So now my question still exists: which wm and gm volumes should I take? Ed On 26 Oct 2010, at 20:40, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Dear Ed, > > to my knowledge, "mris_wm_volume" is the best option to determine the > white matter volume. > > See this wiki page for usage: > http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats > > Best wishes, > Christian > > > --- > Christian Scheel > Department of Psychiatry > University of Cologne > > > > > Am 26.10.2010 15:22, schrieb Ed Gronenschild: >> Hi, >> >> I post this once again because I didn't get any response. >> >> In the v5.0.0 aseg.stats file I can find the following volumes: >> >> - left/right cortical gray matter >> - subcortical gray matter >> - total cortical gray matter >> - total gray matter volume >> and >> - left/right cortical white matter >> - total cortical white matter >> >> How can I derive the total white matter volume? >> >> Ed >

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read data mri_vol2surf
by Oya, Hiroyuki (UI Health Care) 03 Nov '10

03 Nov '10

Hello Is it possible to load the outputs of mri_vol2surf with matlab? Thank you. Hiroyuki

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Re: [Freesurfer] subcortical structure coordinates
by Aya Ben Yakov 31 Oct '10

31 Oct '10

Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) has data 256X256X176, the same dimensions as the original data However, when I convert to nii, and then to brainvoyager format, there's a rotation (perhaps also distortion, but I couldn't see with the rotation), the dimensions don't match (sagittal appears in coronal etc.). When I try to flip the two 256 dimensions, it doesn't help, which means somehow the 176 dimension and the 256 dimension got flipped in the process. If anyone has an idea how to solve this it would be very helpful. Thanks, Aya __________________________________________________ >From Aya Ben Yakov <ayab(a)mail.weizmann.ac.il> Sent Wed 10/27/2010 3:04 PM To Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc freesurfer(a)nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was done on the original data)? Can I convert it back to the original data space? or to talairach? The original data includes only 256X256X176, since there were only 176 slices, yet in mri.vol there are 256 slices. In short - how can I convert correctly to the original space and to talairach? Thanks for your help! Aya __________________________________________________ >From Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent Wed 10/27/2010 2:41 PM To Ørjan Bergmann <orjan.bergmann(a)medisin.uio.no> Cc freesurfer(a)nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt cheers Bruce On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote: > I'm also interested in these segmentations for analysis in Matlab. > > In particular, which volumes should be loaded to get the coordinates of the > segmentations? > > I assume the segmentation volumes are just indices (all voxel belonging to > the same segment are assigned the same unique index), correct ? > > --- > Sincerly, > Dr. Ørjan Bergmann > > > > On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu)>wrote: > >> Hi Aya, >> >> you should be able to convert our segmentations to Nifti, which I assume >> Brainvoyager can read. You can load any of our volumes into matlab with >> either MRIread.m or load_mgh.m and go from there. >> >> cheers >> Bruce >> >> >> On Wed, 27 Oct 2010, Aya Ben Yakov wrote: >> >>> Hi >>> >>> I used FreeSurfer to automatically segment subcortical structures, and I >> would now like to transfer the data to Matlab. I am looking for a way to >> load the coordinates of all structures (or, if it isn't possible, for each >> structure, by its number) to Matlab, in Talairach coordinates. Is this >> possible? If so - how can it be done? >>> >>> I use BrainVoyager, not FSL, for analysis, and I would like to somehow >> use the segmentation from FreeSurfer for analysis in Matlab, in combination >> with data I have from BrainVoyager (the functional data). I don't >> necessarily need talairach coordinates, but otherwise I'm not sure how it >> would be possible to convert between FreeSurfer and BrainVoyager. >>> >>> Any suggestions? >>> Thanks! >>> Aya >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) >> >> >> 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 (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. >> >> > __________________________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) 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 (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.

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What is FreeSurfer V5.0 doing after -wmparc in -autorecon3
by Guang Zeng 30 Oct '10

30 Oct '10

Hi, there, In FS Ver4.5.0, -wmparc is the last step of -autorecon3. Recently, I tested FS Ver5.0, it looks like -wmparc is not the last step of -autorecon3 now, right? I noticed that it still ran several steps after -wmparc, Anyone can give a brief introduction about the -autorecon3 step of FS Ver 5.0? The ReconAllDevTable (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) at FreeSurfer WIKI still is Ver 4.5. Thanks! Zeng

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Source matrix with zero determinant
by Lisa F. Akiyama 29 Oct '10

29 Oct '10

Hello FreeSurfers, I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI Study of Normal Brain Development (Pediatric MRI Study) Repository. However, the command exited with errors mentioning that the source matrix has a zero determinant. I've read past e-mail conversations on this issue, but I did not see any ways of solving this issue. My main goal at the moment is just to perform intensity normalization and skull strip on these data (thus that is why i did not run -notalairach.) When I ran the command listed below on other non-NIH Pediatric MRI data, it performed without any errors. Here is what I ran: > ubuntu:~> *recon-all -autorecon1 -notalairach -s 1433_v1 -i > $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii -force* > INFO: /usr/local/freesurfer/subjects/1433_v1 exists with -i, but -force > specified. > Deleting any previous source volumes > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 todd todd 17815 Oct 28 12:00 > /usr/local/freesurfer/subjects/1433_v1/scripts/recon-all.log > Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 > UTC 2010 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/1433_v1 > > mri_convert > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > > mri_convert > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > INFO: using NIfTI-1 qform > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii... > 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 /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Thu Oct 28 12:01:59 PDT 2010 > Found 1 runs > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > > cp /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > > /usr/local/freesurfer/subjects/1433_v1 > > mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform > > mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform > *MRIresample(): source matrix has zero determinant; matrix is:* > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz... > 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) > Original Data has (0.976562, 0.976562, 0) mm size and (256, 256, 1) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > 0.977 0.000 -0.000 -136.512; > 0.000 -0.977 -0.000 133.512; > 0.000 0.000 0.000 -73.100; > 0.000 0.000 0.000 1.000; > Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 > UTC 2010 x86_64 GNU/Linux > > recon-all -s 1433_v1 exited with ERRORS at Thu Oct 28 12:02:02 PDT 2010 > When I tried to open 001.mgz in tkmedit, as imagined, an error appeared as well: > ubuntu:~> tkmedit 1433_v1 001.mgz > mghRead(/usr/local/freesurfer/subjects//1433_v1/mri/001.mgz, -1): could not > open file > > > Error: Loading volume 001.mgz > > Couldn't read the anatomical volume. > > Tkmedit couldn't read the volume you specified. > This could be because the image format wasn't recognized, > or it couldn't find the proper header, > or the file(s) were unreadable, > or it was the wrong size. > Any help would be greatly appreciated. Thank you in advance. Best, Lisa Akiyama ____________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington

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3 button mouse for macintosh
by Rosso, Isabelle M. 29 Oct '10

29 Oct '10

Hello, Just getting started with Freesurfer. I'm hoping someone can recommend a 3-button mouse that works well with Freesurfer, on a Macintosh. I purchased a Logitech wireless mouse, but can't get it to work properly. Freesurfer does not seem to recognize the 2nd and 3rd buttons as any different than the 1st/left button. So I cannot get edits to work, for example, when trying to edit white matter. Any tips appreciated. -Isabelle --------------------------------------------------------------------- Isabelle M. Rosso, Ph.D. Assistant Professor of Psychology Licensed Psychologist -- Certified Health Service Provider McLean Hospital Neuroimaging Center 115 Mill Street Belmont, MA 02478 Phone: 617.855.2607 Fax: 617.855.2770 irosso(a)hms.harvard.edu ---------------------------------------------------------------------

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How to save a new label after cutting an existing label?
by 李瑾 28 Oct '10

28 Oct '10

Hi freesurfers, I'm trying to generate a new label, from cutting an existed label. The process was shown as attached, First I load a label on fsaverage, lh.inflated, then cut the label along the yellow line and keep the needed part by "cut plane". Now I hope to save the remained label shown in blue in the right pic, into a new label, and use it as my ROI. I tried many methods but they didn't work. Any help would be greatly appreciated. Thank you in advance.

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[Fwd: scientific programmer position with us]
by Douglas N Greve 28 Oct '10

28 Oct '10

Anyone interested should send email to Richard Baumgartner at richard_baumgartner(a)merck.com -------- Original Message -------- Hi Doug, we are urgently looking for a contractor position with us. The person should have good programming skills and some understanding of statistics. He/she will work with imaging, so some imaging experience would be welcome. If you know of someone who might be interested please let me know. Thanks, Richard. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Make functional ROI's from clusters
by Douglas N Greve 28 Oct '10

28 Oct '10

If the labels and data are surface, you can use the --slabel feature. doug Alice Albrecht wrote: > Thanks Doug, > > I have successfully made the labels, but now I want to use those > labels on other data as ROIs and that is where I am having trouble > using the mri_segstats function. I don't see where I can load in my > labels. > > -Alice > > On Thu, Oct 28, 2010 at 2:20 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > As Allison says, you can use the tools listed below. > Alternatively, there is an easier way to do it in tksurfer. > > 1. Click on cluster you want to convert into a label. > 2. Click on the "Custom Fill" button (little paint bucket pouring > into a blue blob). This will popup a window > 3. Click on the "Up to functional values below threshold" box, > then "Fill". The cluster will temporarily turn white, then it will > have a yellow border. You have just created a "label". > 4. Save this label using the File menu. > > doug > > > Allison Stevens wrote: > > Alice, > You might find this tutorial helpful: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividu… > > and mri_volcluster or mri_surfcluster > > Allison > > > > > -- > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Make functional ROI's from clusters
by Alice Albrecht 28 Oct '10

28 Oct '10

Hi Everyone, I'm new to freesurfer so I apologize if my question has already been answered previously (I searched the list archive and the website and couldn't find an answer). I would like to make functionally defined ROIs for each of my subjects based on a localizer I used. I would like to select several ROIs from one contrast. I have done that by simply drawing the ROI on the significant voxels using the "select voxels tool" and saving that out as a label. This process is rather painstaking though, and I was wondering if there was an easier way to do this- perhaps by selecting an entire cluster of voxels at once and saving that out to a label? If anyone has figured out a more efficient way to do this I would appreciate it. Thanks! -Alice

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Freesurfer October 2010