[Freesurfer] hippocampal subfields
Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRIhttps://surfer.nmr.mgh.harvard.edu/pub/articles/VanLeemputHippocampus2009.pdf. suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki ___ 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] How to define a new label for aparc+aseg.mgz in FreeView
Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ 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] Convert expert segmentation to FreeSurfer space
Hi all, I've performed FS subcortical segmentation and my purpose is to use these segmentations as seeds to another method. As FS uses GCA atlas to perform subcortical segmentation, I want to know if the *aseg.mgz* output is in GCA atlas space, or in original space except that the dimensions are 256x256x256, 1mm. On the other hand, I also need to convert expert segmentations in native space to GCA atlas space, that is, the inverse of the process explained in http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I don't know if there is a command to do so, or we have to use a transformation matrix. In the latter case, FreeSurfer creates several tranformation matrices: talairach.lta, talairach.xfm, talairach.m3zbut it's is not clear which one I should use. Thank you in advance!! ___ 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] How to define a new label for aparc+aseg.mgz in FreeView
Hi Emad do you mean draw one manually or add it so it is automatically labeled in new subjects? If the latter it requires manually labeling a training set and rebuilding a classifer, etc..., so it is far from trivial cheers Bruce On Mon, 3 Mar 2014, Emad Ahmadi wrote: Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ 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] Convert expert segmentation to FreeSurfer space
Hi Mohamed the segmentations are in the individual subject conformed space. The talairach.m3z is what is used to transform GCA to the conformed coords cheers Bruce On Mon, 3 Mar 2014, Mohamed Oualid Benkarim wrote: Hi all, I've performed FS subcortical segmentation and my purpose is to use these segmentations as seeds to another method. As FS uses GCA atlas to perform subcortical segmentation, I want to know if the aseg.mgz output is in GCA atlas space, or in original space except that the dimensions are 256x256x256, 1mm. On the other hand, I also need to convert expert segmentations in native space to GCA atlas space, that is, the inverse of the process explained in http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I don't know if there is a command to do so, or we have to use a transformation matrix. In the latter case, FreeSurfer creates several tranformation matrices: talairach.lta, talairach.xfm, talairach.m3zbut it's is not clear which one I should use. Thank you in advance!! ___ 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] Problematic dilated ventricles
I think that it should. To be safe, I would cp aseg.auto.mgz aseg.mgz otherwise aseg.mgz will not change (any differences will be interpreted as manual changes) doug On 03/02/2014 10:07 AM, Bruce Fischl wrote: Hi Victor hmmm, I'm not sure why that didn't work. Perhaps someone else can comment? Doug or Nick: if the aseg.mgz is recreated and you start with -autorecon2-cp shouldn't it propagate the effects of the new aseg forward? cheers Bruce On Thu, 27 Feb 2014, Victor Kovac wrote: Dear Bruce, Have you had any time to try to analyze our subject MPS2002-3? I believe you mentioned you would give it a shot in your free time a couple of months ago. Also, you were kind enough to analyze a subject for me, MPS1036-1, and sent me aseg.auto_noCCseg.new.mgz. I replaced the original file and removed thee new within the title, and then, to re-create the pial and wm surfaces, I ran: set mdir=$SUBJECTS_DIR/MPS1036-1/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta MPS1036-1 cp aseg.auto.mgz aseg.mgz and then: recon-all -autorecon2-cp -autorecon3, which I believe starts the recon-all pipeline at normalization2, as you suggested. However, this has yielded no effect that I can see when I visualize the subject with tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Any advice would be greatly appreciated! Attached is the recon-all.log for this subject. Let me know if I should cc the group. Thank you. Victor On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Victor for each subject I think you want to run: set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz then run recon-all from normalization2 forward (check the recon-all -help for these steps) cheers Bruce On Tue, 7 Jan 2014, Victor Kovac wrote: Hi Bruce, I ran recon-all -autorecon2-cp -autorecon3 -s MPS1036-1 but, again, this did not affect the pial or wm surfaces. I have attached the recon-all.log in case that would be helpful in diagnosing the issue. Any advise would be greatly appreciated. Thanks! Victor On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Victor you can look in the recon-all -help and run the stages that are after mri_ca_label. Not sure why -make all didn't work, perhaps Zeke and/or Nick can comment? Bruce On Thu, 2 Jan 2014, Victor Kovac wrote: Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz then run: recon-all -make all -s MPS1036-1 you should be all set Bruce On Mon, 9 Dec 2013, Victor Kovac wrote: I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you for looking into MPS2002-3 -- it is quite the brain. And somehow, with all those morphological abnormalities, this subject has an IQ of 130. Very
Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss
Try sending me another file (even junk.mgh). Until I get a valid file, I cannot do much doug On 03/01/2014 02:14 AM, charujing123 wrote: Hi doug, Thanks very much doug for your help all the time. I try mri_convert rh.38sb_score.10.mgh junk.mgh,and it display this: = mri_convert rh.38sb_score.10.mgh junk.mgh mri_convert rh.38sb_score.10.mgh junk.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from rh.38sb_score.10.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to junk.mgh... == I found junk.mgh after this done. So it worked. And I have many files like rh.38sb_score.10.mgh(i.e. rh.allsb_score.10.mgh, rh.36sb_score.10.mgh), all of these files have the same question. Doug, I donot know why.As it creates *.y.ocn.dat for only one cluster, may I try this: 1,generate a mask which only has one cluster from ocn.mgh:mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh 2,The run mri_glmfit with --mask cluster2.mgh 3,Then run mri_glmfit-sim with simulation 4,So there is only one cluster in the *.cluster.summary, so it can create a *.y.ocn.dat. 5,So I can use this *.y.ocn.dat file to get the time course of specific cluster. Doug, is that appropriate, or is there any method to deal with my question? Thanks. All the best. Rujing Zha 2014-03-01 charujing123 *发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-03-01 00:20 *主题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄送：* There appears to be something wrong with rh.38sb_score.10.mgh. Try running this mri_convert rh.38sb_score.10.mgh junk.mgh If that fails, then regenerate rh.38sb_score.10.mgh On 02/27/2014 08:12 PM, charujing123 wrote: Hi doug, Thanks doug. I try to ftp by this manu,so I think server is surfer.nmr.mgh.harvard.edu: $ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-15.7x.legacy) ready. Name (surfer.nmr.mgh.harvard.edu:fsurfer): anonymous 331 Guest login ok, send your complete e-mail address as password. Password: 230 Guest login ok, access restrictions apply. Remote system type is UNIX. Using binary mode to transfer files. ftp this information is available on the website:http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange All the best. Rujing Zha 2014-02-28 charujing123 *发件 人：*Douglas N Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-02-28 01:01 *主题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit- sim when using --bg and doss *收件 人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄送：* what server? On 02/27/2014 02:14 AM, charujing123 wrote: Hi doug, As file drop fail to me, so I try use ftp. And it work. I sent these 2 files in the server. Thanks doug.Looking forward your help. ALL the best. Rujing Zha 2014-02-27 charujing123 *发 件 人：*Douglas N Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-02-27 01:54 *主 题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit- sim when using --bg and doss *收 件 人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄送：* Can you send me rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh and /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh through our file drop https://gate.nmr.mgh.harvard.edu/filedrop2 On 02/26/2014 01:16 AM, charujing123 wrote: Hi doug, OK. Terminal output of mri_glmfit-sim --glmdir ../ --no-sim mc-z.neg.3 --cwpvalthresh */0.5/* is included in */file1/*, which cannot create something.y.ocn.dat as its several clusters. Terminal output of mri_glmfit-sim --glmdir ../ --no-sim mc-z.neg.3 --cwpvalthresh */0.1/* is included in */file2/*, which can create something.y.ocn.dat as it has only one cluster. Thanks. All the best. Rujing Zha 2014-02-26 charujing123 * 发 件 人：*Douglas N Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-02-26 00:29 * 主 题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit- sim when using --bg and doss *收 件
Re: [Freesurfer] WM vol as measure
Dear all, I notice that there is a file called wmparc_stats.txt http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhitematterparcellationvolumes Is it possible to get corresponding WM info for a given label? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/2/14 7:18 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] WM vol as measure
That is the jacobian of the white matter surface when it is registered to fsaverage (not related to the actual white matter). On 03/02/2014 08:40 PM, Yang, Daniel wrote: Hi FreeSurfers, A related question (I can't find the answers on the FS website): what's jacobian_white (as a measure)? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 3/2/14 7:18 PM, Yang, Daniel yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM vol as measure
you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] WM vol as measure
Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] WM vol as measure
It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsgd plots 2 Class
Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but I included the error below just in case). Should I just read in the thickness file in matlab/python and pull the data out from there (I assume it each frame is an input ordered respectively to the fsgd)? Thanks, Dan Is all of the data ingdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd Could not find XAxis tag in file. Using default one. �NggdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named marcie.nmr.mgh.harvard.edu by dwakeman Mon Mar 3 13:06:37 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ 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] Freeview crashes xterm
Hi, I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the installation was successful and the paths are set correctly. However, my xterm crashes when I try to launch freeview. Strangely, the program works as expected when launched remotely via NX. Has anyone encountered this problem before? Thanks. - Archana ___ 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] fsgd plots 2 Class
Hi Dan, I have not tried the FSGD plot in freeview yet. You can certainly do the matlab/python thing. The order is the same as in the fsgd file. doug On 03/03/2014 01:17 PM, dgw wrote: Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but I included the error below just in case). Should I just read in the thickness file in matlab/python and pull the data out from there (I assume it each frame is an input ordered respectively to the fsgd)? Thanks, Dan Is all of the data ingdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd Could not find XAxis tag in file. Using default one. �NggdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named marcie.nmr.mgh.harvard.edu by dwakeman Mon Mar 3 13:06:37 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Freeview crashes xterm
My apologies, I meant the X server crashes, not the xterm. Thanks. - Archana -Original Message- From: Venkataraman, Archana Sent: Monday, March 3, 2014 1:19 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Freeview crashes xterm Hi, I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the installation was successful and the paths are set correctly. However, my xterm crashes when I try to launch freeview. Strangely, the program works as expected when launched remotely via NX. Has anyone encountered this problem before? Thanks. - Archana ___ 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] WM vol as measure
Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] WM vol as measure
I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Resting State Networks on Cortical Surface
you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug On 03/02/2014 04:21 AM, Xuelong Zhao wrote: Hi, I am trying to display the 20 ICA components in this nifti file http://brainmap.org/icns/maps.zip onto anatomical template they've provided here http://brainmap.org/icns/colin_tlrc_1x1x1.nii My question is: How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface? Thanks! ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] WM vol as measure
Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
Re: [Freesurfer] WM vol as measure
yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote: Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___
Re: [Freesurfer] WM vol as measure
Sounds like a lot of work, but thanks for your reply. By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label? Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 2:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote: Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center
Re: [Freesurfer] Group Analysis Questions
Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos That's great. Thanks a lot for your help, Doug! Those are the same things. The way you control for age is to compute a value for both groups at the same age (eg, age=0). If you demean the age, then the difference will be at age=meanage. With DOSS, the difference is always the same regardless of age (which makes it more interpretable) doug On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your response. Concerning scenario 2, I believe I have some hard time understanding the term intercept. If I'm not mistaken the intercept represents the cortical thickness at age 0. The resulting clusters by using a design matrix of [1 -1 0 0] will give me the areas where the intercept is significantly different between the Diseased group and the healthy group. Are those clusters the same clusters that have a different mean regional cortical thickness in Diseased versus Healthy subjects after controlling for age, or are those two completely different things? Thanks again, Panos On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? Yes, just a simple two-group t-test. 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Correct, that will give you the difference in age/thickness slopes. You could do [1 -1 0 0] to give you the difference in intercepts. A better way, is to first look for differences in the slopes. If you do not find any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, the difference in intercept is always constant regardless of age (as opposed to DODS). doug Thanks in advance for your help and sorry for the lengthy message. Best, Panos ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
Re: [Freesurfer] WM vol as measure
Right. How do you define the complete WM vol underneath the label? On 03/03/2014 03:01 PM, Yang, Daniel wrote: Sounds like a lot of work, but thanks for your reply. By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label? Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 3/3/14 2:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote: Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote:
Re: [Freesurfer] Group Analysis Questions
no, that is only for plotting On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos That's great. Thanks a lot for your help, Doug! Those are the same things. The way you control for age is to compute a value for both groups at the same age (eg, age=0). If you demean the age, then the difference will be at age=meanage. With DOSS, the difference is always the same regardless of age (which makes it more interpretable) doug On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your response. Concerning scenario 2, I believe I have some hard time understanding the term intercept. If I'm not mistaken the intercept represents the cortical thickness at age 0. The resulting clusters by using a design matrix of [1 -1 0 0] will give me the areas where the intercept is significantly different between the Diseased group and the healthy group. Are those clusters the same clusters that have a different mean regional cortical thickness in Diseased versus Healthy subjects after controlling for age, or are those two completely different things? Thanks again, Panos On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? Yes, just a simple two-group t-test. 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Correct, that will give you the difference in age/thickness slopes. You could do [1 -1 0 0] to give you the difference in intercepts. A better way, is to first look for differences in the slopes. If you do not find any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, the difference in intercept is always constant regardless of age (as opposed to DODS). doug Thanks in advance for your help and sorry for the lengthy message. Best, Panos ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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:
Re: [Freesurfer] error at spmregister
So I'm running spmregister from a new computer now, and I'm still not getting a successful output. I am not longer getting a matlab error, but after I run spmregister, I then run tkregister2 but get an error that it couldn't open spm.reg.dat. It wasn't created in the spmregister I guess. What would be the problem when I ran spmregister Thanks, m From: Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Saturday, March 01, 2014 10:31 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error at spmregister this is a matlab problem, not a FreeSurfer problem, so I'm not sure. It might be the MNE toolbox. I would try commenting out all the non-FS stuff in your ~/matlab/startup.m file and see if the problem goes away. On 3/1/14 8:50 AM, Borzello, Mia wrote: I haven't actually changed anything in the setup though- how do I figure out what to change? Thanks, Mia Sent from my iPhone On Feb 28, 2014, at 7:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: looks like there is something going wrong in your matlab setup Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:UndefinedFunction Undefined function or variable 'mne_setup_toolbox'. On 02/28/2014 12:01 PM, Borzello, Mia wrote: the last line of error_spm is the command line, and the errors for that command are above. Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, February 28, 2014 11:58 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error at spmregister never seen that. can you send your command line and the log file? On 02/28/2014 11:43 AM, Borzello, Mia wrote: Hi Freesurfers, I get an error when using spmregister saying Maximum variable size allowed by the program is exceeded- is that a problem with the number of dicoms? I can attach a screenshot of the error if that helps. Thanks, Mia ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] asegstats2table error
All aseg.stats seems to have volume of 45 ROIs with some hypointensities value =0. Also, I checked aseg.mgz and looks fine with these subjects. I extracted values with asegstats2table with --all-seg flag. I hope that is okay? On Sunday, March 2, 2014 11:28 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: That means that it was expecting to find 66 segmentations but only found 55. Sometimes there are some segmentations in one subject that are not in another (usually hypointensities). But 11 is too many. Have you looked at the aseg to see if it looks right? You can also compare the aseg.stats file to see which segs are missing. doug On 3/2/14 9:46 AM, sabin khadka wrote: Hi all, While using asegstats2table, I got following error for few subjects, WARN SUBID: nmeasure 66, expecting 55 It let me extract cortical thickness and surface area using aparcstats2table though. Any suggestions? -SABIN ___ 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 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] Group Analysis Questions
I see. Thank you no, that is only for plotting On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos That's great. Thanks a lot for your help, Doug! Those are the same things. The way you control for age is to compute a value for both groups at the same age (eg, age=0). If you demean the age, then the difference will be at age=meanage. With DOSS, the difference is always the same regardless of age (which makes it more interpretable) doug On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your response. Concerning scenario 2, I believe I have some hard time understanding the term intercept. If I'm not mistaken the intercept represents the cortical thickness at age 0. The resulting clusters by using a design matrix of [1 -1 0 0] will give me the areas where the intercept is significantly different between the Diseased group and the healthy group. Are those clusters the same clusters that have a different mean regional cortical thickness in Diseased versus Healthy subjects after controlling for age, or are those two completely different things? Thanks again, Panos On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? Yes, just a simple two-group t-test. 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Correct, that will give you the difference in age/thickness slopes. You could do [1 -1 0 0] to give you the difference in intercepts. A better way, is to first look for differences in the slopes. If you do not find any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, the difference in intercept is always constant regardless of age (as opposed to DODS). doug Thanks in advance for your help and sorry for the lengthy message. Best, Panos ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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:
Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView
Hi Bruce, Thank you for your response. I just want to draw manually the region of the new label on the images of few subjects. What I am about to do is to define a new label for the trigeminal nerve sensory nucleus (just roughly as the region that the nerve enters the brainstem); I just need to label it manually for all subjects. Best, Emad On Mar 3, 2014, at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Emad do you mean draw one manually or add it so it is automatically labeled in new subjects? If the latter it requires manually labeling a training set and rebuilding a classifer, etc..., so it is far from trivial cheers Bruce On Mon, 3 Mar 2014, Emad Ahmadi wrote: Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ 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] hippocampal subfields
Dear Gabor, the segmentation benefits to some extent from higher resolution data, but produces decent estimates of the subfields at 1x1x1. We are working on a new atlas that will incorporate much more detail, and will more effectively take advantage of high-resolution images. Kind regards, Juan Eugenio Iglesias On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI. suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki ___ 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.
Re: [Freesurfer] hippocampal subfields
Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: Dear Gabor, the segmentation benefits to some extent from higher resolution data, but produces decent estimates of the subfields at 1x1x1. We are working on a new atlas that will incorporate much more detail, and will more effectively take advantage of high-resolution images. Kind regards, Juan Eugenio Iglesias On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI. suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki ___ 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
[Freesurfer] How to create a figure for a scientific article
Dear Freesurfers, I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2 I would like to create a figure for my article. However, I'm not able to find a way to highlight only cerebellar cortex / white matter with freeview, instead of having every label of other subcortical structures in different colors. I would like to have only the cerebellum colored. Could this be done with freeview ? Thanks a lot, Charles ___ 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] How to create a figure for a scientific article
not sure if it can be done in fv, but you can create a mask of just the cerebellum cortex and wm with mri_binarize (use --match A B, where A and B are the segids for the two ROIs), then use mri_mask to mask everything else out of your segmentation On 03/03/2014 06:01 PM, charles laidi wrote: Dear Freesurfers, I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2 I would like to create a figure for my article. However, I'm not able to find a way to highlight only cerebellar cortex / white matter with freeview, instead of having every label of other subcortical structures in different colors. I would like to have only the cerebellum colored. Could this be done with freeview ? Thanks a lot, Charles ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Export freesurfer data
Dear Bruce and Doug, Thank you very much! Would you please tell me more about what freesurfer data actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness? Thank you very much! Sincerely, Ye On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you be more specific about what you mean by freesurfer data? Each subject has 300MB of data doug On 02/27/2014 10:48 PM, ye tian wrote: Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text? Thank you very much! Sincerely, Ye ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] Resting State Networks on Cortical Surface
Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister. However, I wasn't actually sure if I put the correct input: bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image? Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab? Thanks! Date: Mon, 3 Mar 2014 14:20:55 -0500 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug On 03/02/2014 04:21 AM, Xuelong Zhao wrote: Hi, I am trying to display the 20 ICA components in this nifti file http://brainmap.org/icns/maps.zip onto anatomical template they've provided here http://brainmap.org/icns/colin_tlrc_1x1x1.nii My question is: How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface? Thanks! ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] Compute DTI metrics in NAWM in Tracula
Hi Anastasia
I have finally managed to coregister and resample all lesion masks on DTI
images :-), and as you suggested I set the lesion voxels to 0 in
dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes)
Then the command I found in the trac-all log was the one below
(where TRACT is the full name of the tract and SHORT_TRACT is the short name)
./freesurfer-stable5_3_0-05152013/bin/dmri_pathstats --intrc
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]} --dtbase
${PATH_3T}${SUBJECTS_3T[$subj]}/dmri/dtifit --path
${SHORT_TRACT[$num_tract]} --subj ${SUBJECTS_3T[$subj]} --out
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.overall.txt
--outvox
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/${TRACT[$num_tract]}/pathstats.byvoxel.txt
However I got this error message and couldn't find in the log file how to
set the output type
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: fio_pushd:
${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr
ERROR: must specify at least one type of output
Would you have some idea about that?
Thank you very much
Celine
Hi Celine - That's an interesting question. There's nothing implemented in
there right now that would allow you to skip part of the tract in the
along-the-tract stats. One (not very elegant) way to try to do something
like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero.
(You'll want to save the original volume under some other name for backup
first.) If you want the same for the diffusivities, repeat for the also
for the MD, L1, L2, L3 volumes.
2. Run the dmri_pathstats command line that you'll find in trac-all.log
for that subject.
This will regenerate all the pathstats.* files, but now the parts of the
tract that go through the lesions will have zero values (or very low, if
they're mixed in with some neighboring voxels).
Let us know if this worked! If not I may be able to implement something.
a.y
On Tue, 11 Feb 2014, Celine Louapre wrote:
Hi Anastasia and freesurfer experts,
I am trying to get DTI values along the tracts as in the pathstatbyvoxel
file, but excluding inflammatory WM lesions. I have masks of the WM
lesions that I could apply on the DTI maps, but then how could I compute
the DTI metrics along the tract with the exclusion of the lesion? (I
guess
the last step of trac-all -path could be applied to DTI maps that were
masked by the lesions?)
I would like to keep the advantage of having the DTI weighted metrics in
particular.
Thanks a lot for your help!
Celine
___
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] Matlab help
Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur, ___ 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] Matlab help
Hi! Can you specify what happens when you try to read the files? On 4 mars 2014, at 06:44, Saurabh Thakur srbht...@gmail.com wrote: Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur, ___ 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] Matlab help
Hi Markus Gschwind, I am using Matlab 7.12.0.635 (R2011a), I am not able to read the dicom image neither brain.mgz file nor the surface file in matlab. I have added these file in matlab directory. Comment or error i m getting is : for example : * load_dicom_fl(IM_0001)??? Undefined function or variable 'IM_0001'.* 2nd example : * MRIread(brain.mgz,brainMRI.hdr) ??? Undefined variable brain or function brain.mgz.* I looking forward to work on matlab along with freesurfer. Looking for your reply asap. Thanks for reply. cheers Saurabh Thakur, On Tue, Mar 4, 2014 at 12:17 PM, markus.gschw...@gmail.com wrote: Hi! Can you specify what happens when you try to read the files? On 4 mars 2014, at 06:44, Saurabh Thakur srbht...@gmail.com wrote: Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur, ___ 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 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] Matlab help
Hi Saurabh,
On Mar 4, 2014, at 07:56 , Saurabh Thakur srbht...@gmail.com wrote:
Hi Markus Gschwind,
I am using Matlab 7.12.0.635 (R2011a),
I am not able to read the dicom image neither brain.mgz file nor the surface
file in matlab.
I have added these file in matlab directory.
Comment or error i m getting is :
for example :
load_dicom_fl(IM_0001)
??? Undefined function or variable 'IM_0001'.
2nd example :
MRIread(brain.mgz,brainMRI.hdr)
??? Undefined variable brain or function brain.mgz.
You need to supply the full path to the volumes in a string, so
assuming you called matlab from the same directory where brain.mgz is located,
or used mat lab's cd('/patrh/to/your/data') to make sure you are there. Then
simply calling MRIread('brain.mgz'); should do the trick; note: only put the
stuff between the double quotes into the matlab command window.
best
Sebastian
I looking forward to work on matlab along with freesurfer.
Looking for your reply asap.
Thanks for reply.
cheers
Saurabh Thakur,
On Tue, Mar 4, 2014 at 12:17 PM, markus.gschw...@gmail.com wrote:
Hi!
Can you specify what happens when you try to read the files?
On 4 mars 2014, at 06:44, Saurabh Thakur srbht...@gmail.com wrote:
Hello Freesurfer,
I am trying to runs MRIread.m file in matlab.
But it is not reading the brain.mgz or any other format.
Can u help in this regards.
Thanks in advance,
cheers
Saurabh Thakur,
___
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
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
