Re: [Freesurfer] Are cortical thickness and surface area independent of each other?
do you mean independent in the statistical sense? Certainlty the way in which they are computed is independent, and in principle they should not depend on each other cheers, Bruce On Mon, 4 Oct 2010, Jürgen Hänggi wrote: Dear FS experts I would like to know whether cortical thickness and cortical surface area as computed by FS are independent of each other. My guess is that they are not independent, isn't it? Regards Jürgen Jürgen Hänggi, Ph.D. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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] Are cortical thickness and surface area independent of each other?
Dear FS experts I would like to know whether cortical thickness and cortical surface area as computed by FS are independent of each other. My guess is that they are not independent, isn't it? Regards Jürgen Jürgen Hänggi, Ph.D. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Making a surface from the skull?
Thanks for these suggestions - looks promising so far! mjp On Oct 1, 2010, at 4:32 PM, Nick Schmansky wrote: also, once you get a surface file, then mris_convert will convert to .stl format, which we've used in 3d printer applications. if you can get a skull from mri_watershed, then mri_tessellate will make a surface. mris_smooth and mris_keep_main_component are two other useful utility to clean things up. n. On Fri, 2010-10-01 at 16:24 -0400, Bruce Fischl wrote: Hi Mark, you might check Matti Hamalainen's MNE website. He uses the watershed code to generate boundary models, including skull. Or just try out mri_watershed with -surf I think (it's covered in the help, at least a bit) cheers Bruce On Fri, 1 Oct 2010, Mark J. Pearrow wrote: Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant. Best, mjp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] spmregister error
Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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] spmregister error swoodman o Re: [Freesurfer] spmregister error Adam Nitenson + Re: [Freesurfer] spmregister error Douglas N Greve # Re: [Freesurfer] spmregister error swoodman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] spmregister error
Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] problem with tksurfer display
Have you tried updating your video driver? What kind of video card to you have? On Sat, 2 Oct 2010, [gbk] ²ýÃ÷ wrote: Dear Freesurfers£º When I display and edit surfaces with tksurfer, the image can be loaded correctly, but whenever i rotate it, load curvatures, or load patches, it always freezes after my first operation and can't continue with the next operations. The freesurfer version i use is FS 4.5.0 under Fedora core 12, and the woking momory of computer is 4 Gigabytes with 4 processors, also enough hard disk space is available. can someone tell my what the problem is, and how i can fix it? thank you very much! changming___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32
Siti, can you give us the full command-line (without the variables) and the full terminal output? doug Siti Hajar wrote: When I ran this command, mri_segstats --seg $fsaveragesurfpath/$hemi.fsaverage.$hemi_$roi_$subj.mgh --in $hemi.thickness.fsaverage.mgh --sum segstats-$hemi_$roi_$subj.txt, this kind of output came out mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, -1): could not open file-- which indicated that there was no lh.thickness.fsaverage.mgh created. Well, basically, when I ran recon-all, lh.thickness.fsaverage.mgh should be created, but it wasn't. So, again with my question,is this situation happened due to the new freesurfer software that I installed or was it caused by other source? The skull strip result was ok *From:* freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, September 20, 2010 9:49:16 PM *Subject:* Freesurfer Digest, Vol 79, Issue 32 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@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-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu mailto:freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. Re: mri_label2volume issues (Michael Waskom) 2. Generating a 'non-zero' group mask (Marco Loggia, PhD) 3. Re: recon-all quality control checks on largenumbersof subjects (Nick Schmansky) 4. lh.thickness.fsaverage (Siti Hajar) 5. Re: lh.thickness.fsaverage (Douglas Greve) -- Message: 1 Date: Fri, 17 Sep 2010 11:04:00 -0400 From: Michael Waskom mwas...@mit.edu mailto:mwas...@mit.edu Subject: Re: [Freesurfer] mri_label2volume issues To: Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Message-ID: aanlkti=5znihxybqu0wwf-ysjn6opoqk2bfuf2_ii...@mail.gmail.com mailto:5znihxybqu0wwf-ysjn6opoqk2bfuf2_ii...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Prapti, Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly. The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run: mri_binarize --i your_annot_name+aseg.mgz --match that voxel value --o you_roi_name.mgz Which will have 1s where your ROI is and 0s everywhere else. Best, Mike ---Original Message--- Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this. As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize? Thanks, Prapti -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere. doug Prapti Gautam wrote: Hi Doug, Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my label into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this? Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg? Thanks, Prapti -- Message: 2 Date: Fri, 17 Sep 2010 11:38:22 -0400 From: Marco Loggia, PhD
Re: [Freesurfer] QDEC 5.0 with data from 4.x recon-all data
You can say 4.x. The statistical part did not change that much in version 5. doug Manabu Kubota wrote: Hi, I'm interested in this issue. If I use a former FreeSurfer version (ver. 4.x) for all the preprocessing of each data and apply the new QDEC in FreeSurfer ver. 5.0.0 JUST to make analyses easier (say, use of mri_glmfit-sim), do I have to specify both FreeSurfer ver. 4.x and FreeSurfer 5.0.0 (or QDEC ver 1.4) in the methodological section of research manuscripts? Or is it enough to mention FreeSurfer ver. 4.x (and mri_glmfit-sim) for the analyses? Best regards, Manabu Graduate school of medicine, Kyoto University 2010/10/1 Nick Schmansky ni...@nmr.mgh.harvard.edu: yes, you may use v5 qdec with prior processed data. n. On Thu, 2010-09-30 at 21:04 +0200, Christian Scheel wrote: Dear Mira, I posted a similar question some days ago. It seems to be possible to use the new qdec version for the group analysis for data that has been processed and cached with version 4.x (at least 4.05 and newer). Check this posting in the mailing archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15166.html Best wishes, Christian --- Christian Scheel University of Cologne Department of Psychiatry Am 30.09.2010 20:45, schrieb Mira Michelle Raman: Hi, I was wondering if it were possible/advisable to use data processed and cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it has enhanced capabilities. Sincerely, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] normal brain volume ?...
Hi: I am quantifying the brain volume of some MS patients (BrainSegVol-ventricles-cerebelum-brain_stem)... There exist any paper that shows normal brain volume ?... There exisst any other way to compute the brain volume ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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] BEM surfaces
Dear experts, Currently I am playing around with the mri_watershed algorithm. After processing the T1.mgz from bert I got 256 COR files plus the COR-.info with the direction cosine information. mri_watershed -surf -useSRAS $SUBJECTS_DIR/bert/mri/T1.mgz $SUBJECTS_DIR/bert/bem/ Output in bert/bem/: COR-.info, COR-001 . COR-256 How can extract the information of these files which I need to proceed .mesh files in Matlab? Thank you so much in advance. Sincerely, Alexander ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
