[Freesurfer] (no subject)
-- Dott.ssa Valentina Ciullo Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39(0)651501101 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.comhttp://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli ___ 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] Transparency surface
Dear Freesurfer experts, Using tksurfer I open an inflated surface and I display the pial surface. Then I load an overlay but I'm not able to see it correctly. Is it possible to put a transparency/opacity value for the surface so I can see better my overlay ? Thank you for your help Arnaud Bore ___ 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] missing eTIV in asegstats2table
Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani ___ 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] Question about preproc-sess -no-subcort-mask
Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- 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] missing eTIV in asegstats2table
It should still be there. I changed the name to EstimatedTotalIntraCranialVol, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani ___ 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] Question about preproc-sess -no-subcort-mask
Hi Doug, Here it is. cheers, Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 5:53 PM Subject: Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- 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/ 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. preproc-sess Description: Binary data ___ 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] Transparency surface
Hi Arnaud why would transparency help? You should be able to view the overlay on any surface without transparency (the overlay defines the colors displayed on the surface). Can you explain further why the normal display in tksurfer doesn't do what you want? cheers Bruce On Tue, 1 Oct 2013, Arnaud Boré wrote: Dear Freesurfer experts, Using tksurfer I open an inflated surface and I display the pial surface. Then I load an overlay but I'm not able to see it correctly. Is it possible to put a transparency/opacity value for the surface so I can see better my overlay ? Thank you for your help Arnaud Bore ___ 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 questions
Simply to make sure, 1) Is there no way that one can edit two volumes simultaneously similarly to tkmedits aux+main volume brush? 2) When editing voxels in freeview, is there anyway to have the cursor behave the same way it does in navigation mode. That is, I'd like to be able to see exactly where I'm editing in all 3 views, rather than just the one I'm editing in. Best, Jon ___ 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] Question about preproc-sess -no-subcort-mask
I have to say that I'm stumped. Do you really need to resolve this question? doug On 10/01/2013 12:27 PM, Leila Reddy wrote: Hi Doug, Here it is. cheers, Leila *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Leila Reddy le...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 5:53 PM *Subject:* Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: 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 Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- 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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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
Re: [Freesurfer] MNI152 to 305 conversion
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug ps. You can try using the reorder feature in mri_convert, but it will be trial and error. On 10/01/2013 11:55 AM, Paul Beach wrote: Ah! Yes. I changed directories to my subjects_dir and the command worked. I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz \/ /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview. On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Oh I see. You probably don't have write access to the current directory (which I assume to be //extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory. --Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, You have to give it the full path: /mri_convert ///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/ On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /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 mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, Ok. Do a mri_convert mni305.cor.mgz mni305.nii.gz. How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine I'm not sure if that clarifies anything, though. On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, Just to clarify, 1) If you load
Re: [Freesurfer] Freeview questions
Hi Jon, 1) No, there is no way to do that in freeview. 2) In Editing mode, you can use shift+ctrl+Left mouse button to move the cursor. Ruopeng On 10/01/2013 12:50 PM, Jonathan Holt wrote: Simply to make sure, 1) Is there no way that one can edit two volumes simultaneously similarly to tkmedits aux+main volume brush? 2) When editing voxels in freeview, is there anyway to have the cursor behave the same way it does in navigation mode. That is, I'd like to be able to see exactly where I'm editing in all 3 views, rather than just the one I'm editing in. Best, Jon ___ 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] Repost: pcc maps and mri_glmfit
Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? *Is the average r-value or z-value saved somewhere? *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar ___ 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] Question about preproc-sess -no-subcort-mask
Hi Doug, Now that I know that I wasn't inadvertently making a stupid mistake in my analysis, and I also know how to get around the problem, I don't really need to solve it anymore. Thanks for your time. Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 6:57 PM Subject: Re: Question about preproc-sess -no-subcort-mask I have to say that I'm stumped. Do you really need to resolve this question? doug On 10/01/2013 12:27 PM, Leila Reddy wrote: Hi Doug, Here it is. cheers, Leila *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Leila Reddy le...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 5:53 PM *Subject:* Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: 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 Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- 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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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
Re: [Freesurfer] Transparency surface
Hi, Is there a way to see both side of the activation with a brain which looks like the pial ? Without inflated maybe I'm not really familiar with tksurfer. So far I used tksurfer fsaverage6 lh inflated by default. Thank you. Arnaud 2013/10/1 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Arnaud can you in general cc the list on these questions so that others can answer. What you are trying to do is what the inflated surface is designed for. I don't think the transparency thing would work - it would just be confusing cheers Bruce On Tue, 1 Oct 2013, Arnaud Boré wrote: Hi Bruce, I added two pictures so you can see what I referred to. When I display the main surface, I'm able to see my activation. But when using the pial surface, it's hard to see the activation. I thought that if I could change the transparency of the surface, I will be able to see the other side (i.e., hidden in the sulci) of the activation (as shown in the main surface). Thank you for your answer. Arnaud 2013/10/1 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Arnaud why would transparency help? You should be able to view the overlay on any surface without transparency (the overlay defines the colors displayed on the surface). Can you explain further why the normal display in tksurfer doesn't do what you want? cheers Bruce On Tue, 1 Oct 2013, Arnaud Boré wrote: Dear Freesurfer experts, Using tksurfer I open an inflated surface and I display the pial surface. Then I load an overlay but I'm not able to see it correctly. Is it possible to put a transparency/opacity value for the surface so I can see better my overlay ? Thank you for your help Arnaud Bore 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/**compliancelinehttp://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. -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 ___ 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] co-registration: SWI images with FLAIR
Dear All, Can I co-register SWI with FLAIR images using Freesurfer? thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ 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] co-registration: SWI images with FLAIR
yes, bbregister should do this just fine with T2 contrast specified cheers Bruce On Tue, 1 Oct 2013, Ayaz, Muhammad wrote: Dear All, Can I co-register SWI with FLAIR images using Freesurfer? thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ 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] Hippocampal subfield segmentation paused
Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene___ 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 subfield segmentation paused
Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] Repost: pcc maps and mri_glmfit
On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar ___ 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] Xhemi-Fsaverage Vs myatlas
I'm not sure I understand what you mean by that. Your inflated brain just needs to be inflated a little more to get the folds out of it. I cannot tell whether this is sufficient or not. I found that I had to iterate many times (on the order of 30) to get stable results. This is quite burdensome, esp with 86 subjects. Have you tried using fsaverage_sym? doug On 10/01/2013 05:59 AM, amirhossein manzouri wrote: Dear FS experts, I want to perform asymmetry study in a group of subjects. I have created myatlas.i3 from my data(86) based on the procedure from Xhemi page and tksurfer lh inflated of both fsaverage and myatlas image is attached! it has shown that my atlas is smaller in general and larger in temporal lobe! I wonder if this is correct and I can proceed to compare left and right Hemispheres? -- Best regards, Amirhossein Manzouri ___ 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] overlay mni152 activation -- difference between tksurfer and freeview
Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] overlay mni152 activation -- difference between tksurfer and freeview
The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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. ___ 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] DODS slope information
If you are using mri_glmfit, just set up contrasts to test each individual slope vs zero. doug On 09/27/2013 12:04 PM, Jacobs H (NP) wrote: Hi Freesurfers, I just looked at my cortical thickness results, in which I performed an interaction between group (2 groups) and cognition (continuous). I see regions popping up, which is great! Especially since they are related to the task. Now, I made a scatterplot of some of these vertices to get a better understanding of the effect. However, I am wondering how I can figure out if the slope within each group is significant. How can I examine that? Thanks! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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] overlay mni152 activation -- difference between tksurfer and freeview
Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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. ___ 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:
Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview
I don't understand what you mean by a much smaller brain. Can you elaborate? On 10/01/2013 06:10 PM, Yang, Daniel wrote: Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu%3E wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 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: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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
[Freesurfer] rh or lh?
Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] overlay mni152 activation -- difference between tksurfer and freeview
I thinkyou just need to change the aparc to be either transparent or outline. On 10/01/2013 07:44 PM, Yang, Daniel wrote: Hi Doug, I think I find out where the problem is. Actually the mri_vol2surf works nicely (and it's also true that tksurfer with -mni152reg samples the overlay to the white surface by default instead of to the pial surface.) The problem is in freeview + rh.aparc.annot. If you do the following for the attached rh mgh file, you will see it correctly displayed: tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh If you overlay this mgh in freeview with rh.inflated surface, but without loading rh.aparc.annot, it also displays correctly. However, once I load the rh.aparc.annot, I see something like attached png. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand what you mean by a much smaller brain. Can you elaborate? On 10/01/2013 06:10 PM, Yang, Daniel wrote: Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:00 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: The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu%3E mailto:yung-jui.y...@yale.edu%3E%3E wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 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: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between
Re: [Freesurfer] rh or lh?
Not really. If this is an individual subject, you can look at the number of vertices and see whether it matches lh or rh. For fsaverage, the number of vertices is the same for lh and rh. On 10/01/2013 07:45 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] MNI152 to 305 conversion
Hi Doug, except Paul was saying the mni305.cor.mgz does not show up correctly in freeview as well. Doesn't freeview handle header orientation information properly? --Thomas On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug ps. You can try using the reorder feature in mri_convert, but it will be trial and error. On 10/01/2013 11:55 AM, Paul Beach wrote: Ah! Yes. I changed directories to my subjects_dir and the command worked. I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz \/ /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview. On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Oh I see. You probably don't have write access to the current directory (which I assume to be //extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory. --Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, You have to give it the full path: /mri_convert ///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/ On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /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 mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, Ok. Do a mri_convert mni305.cor.mgz mni305.nii.gz. How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine I'm not sure if that clarifies anything, though. On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo
Re: [Freesurfer] MNI152 to 305 conversion
Hi Thomas, it loads properly for me. doug On 10/01/2013 08:21 PM, Thomas Yeo wrote: Hi Doug, except Paul was saying the mni305.cor.mgz does not show up correctly in freeview as well. Doesn't freeview handle header orientation information properly? --Thomas On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug ps. You can try using the reorder feature in mri_convert, but it will be trial and error. On 10/01/2013 11:55 AM, Paul Beach wrote: Ah! Yes. I changed directories to my subjects_dir and the command worked. I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz \/ /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview. On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Oh I see. You probably don't have write access to the current directory (which I assume to be //extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory. --Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, You have to give it the full path: /mri_convert ///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/ On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /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 mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu wrote: Hi Paul, Ok. Do a mri_convert mni305.cor.mgz mni305.nii.gz. How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
[Freesurfer] UPDATES on Brainhack 2013 (including stipend application extension)
Dear All, Brainhack 2013 will be taking place in just under a month outside of Paris, France. A welcome reception will be held on the evening of October 23rd to be followed by the hackathon on October 24th, 25th, and 26th. Brainhack 2013 will be highlighted by Ignite talks by: - *Yves Burnod, PhD,http://www.imed.jussieu.fr/en/outils/affiche_personne.php?pers_id=217 INSERM (French national Institute for Health)* - *Jean Daunizeau, PhD,https://sites.google.com/site/jeandaunizeauswebsite/l’Institut du Cerveau et de la Moelle épinière* - *Martin Lindquist, PhD, http://www.biostat.jhsph.edu/~mlindqui/ Department of Biostatistics of the Johns Hopkins University Bloomberg School of Public Health.* - *Ziad Saad, PhD,http://intramural.nimh.nih.gov/research/clinicians/sc_saad_z.html US National Institutes of Mental Health Statistical and Scientific Computing Core* - *Gaël Varoquaux, PhD, http://gael-varoquaux.info/ INRIA at the Neurospin* - *Xinian Zuo, PhD, http://lfcd.psych.ac.cn/ Institute of Psychology, Chinese Academy of Science* UPDATES: We have four important updates about Brainhack 2013: (1) Brainhack.org back online after being offline at the end of last week and over the weekend. Details about Brainhack 2013 can now be found there. (2) Due to the technical problems last week, we've extend the stipend application deadline to 11:59 PM EST on Thursday October 3rd. See brainhack.org for details on how to apply. (3) Attendees can now complete their registration by paying the registration fees at: http://dr01.azur-colloque.cnrs.fr Instructions on this process can be found here: http://www.brainhack.org/?page_id=5425. The deadline for registering is October 15th and payment must be received by October 16th. (4) If you want to have your poster abstract appear in the Brainhack 2013 Program, please submit your abstract online at brainhack.org. Posters will be presented electronically during the welcome reception. Hope to see you next Month. Please let Donald McLaren know if you have any questions. He can be reached via email: mclaren.don...@gmail.com ___ 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.
