[Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
Dear FreeSurfer Users; I am quite new to FreeSurfer and have just downloaded the full package. However; I do have a serious problem with introducing the license file to the system. The Freesurfer registration e-mail doesnot have any attachments but tells me to 'Place the three lines between the CUT HERE markers in a file named .license in the directory pointed to by the $FREESURFER_HOME environment variable' Am I supposed to cut and copy the three lines into the LICENSE file (I tried but was not allowed to make changes in it)? Or am I supposed to create a new file with an extension .license and copy it into the freesurfer folder? ( May seem irrelevant but I copied the LICENSE file to desktop; delete everything and put only the three lines between CUT HERE markers and saved the file with a .license extension and put it in the freesurfer directory- but it didnot help.) Your help is greatly appreciated. Thank you Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named .license in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---CUT HERE--- berdoga...@gmail.com 11403 *CQmdQSakwEaM #---CUT HERE--- The information you submitted was: title=Ms firstname=Sinem Burcu lastname=ERDOGAN institution_name=Bogazici University institution_type=nonprofit_education_research user_email=berdoga...@gmail.com address1=Bogazici Universitesi Biyomedikal Muh. Enstitusu Kandilli Kampus Cengelkoy address2=Kandilli Kampus rasathane cengelkoy city=Istanbul state=Uskudar zipcode=34684 country=turkey telephone=+905333965220 fax= OS/Platform=Darwin/Mac ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdo...@boun.edu.tr ___ 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] Modifying Regression Analysis
I'm not sure how I could do that considering that, in the paradigm file, the 1, 3, 5, and 7 loads are all designated with the same condition number (2), while the weight is what varies. My current contrast (2vFix) encompassed all four loads so I'm not sure how I could just make a new contrast without altering the condition number for the 7-load, and thus requiring a new analysis. -Adam Hi Adam, why not just make a new contrast with 1, 3, and 5? You can then run selxavg3-sess -- it will recognized that you only added a contrast and just re-run the contrast (should be pretty quick). doug Adam Nitenson wrote: Hi Doug and Freesurfers, I am currently analyzing data acquired from the Sternberg memory task, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single contrast. My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data. From looking at the analysis setup, it looks like I would have to make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the 2s in the paradigm file to 1s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially ignore the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ 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 do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
Hi Sinem you need to create a file named $FREESURFER_HOME/.license with the contents begin the stuff between the CUT HERE lines: erdoga...@gmail.com 11403 �*CQmdQSakwEaM if you don't have permission to create it you need to talk to your sysadmin about creating it. cheers Bruce On Tue, 9 Aug 2011, Sinem Burcu Erdo?an wrote: Dear FreeSurfer Users; I am quite new to FreeSurfer and have just downloaded the full package. However; I do have a serious problem with introducing the license file to the system. The Freesurfer registration e-mail doesnot have any attachments but tells me to 'Place the three lines between the CUT HERE markers in a file named .license in the directory pointed to by the $FREESURFER_HOME environment variable' Am I supposed to cut and copy the three lines into the LICENSE file (I tried but was not allowed to make changes in it)? Or am I supposed to create a new file with an extension .license and copy it into the freesurfer folder? ( May seem irrelevant but I copied the LICENSE file to desktop; delete everything and put only the three lines between CUT HERE markers and saved the file with a .license extension and put it in the freesurfer directory- but it didnot help.) Your help is greatly appreciated. Thank you Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named .license in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---CUT HERE--- berdoga...@gmail.com 11403 *CQmdQSakwEaM #---CUT HERE--- The information you submitted was: title=Ms firstname=Sinem Burcu lastname=ERDOGAN institution_name=Bogazici University institution_type=nonprofit_education_research user_email=berdoga...@gmail.com address1=Bogazici Universitesi Biyomedikal Muh. Enstitusu Kandilli Kampus Cengelkoy address2=Kandilli Kampus rasathane cengelkoy city=Istanbul state=Uskudar zipcode=34684 country=turkey telephone=+905333965220 fax= OS/Platform=Darwin/Mac ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Sinem Burcu ERDO?AN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / ?STANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdo...@boun.edu.tr ___ 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] Segmentation of hippocampal subfilelds
Hi Mohan, The segmentation results are given as probability maps: a (unsigned 8-bit) value of 0 means probability 0 , 255 means probability 1, and everything in between scales linearly. The proper way to obtain crisp label maps from these images is to assign each voxel to the label map that has the highest probability, so you'd need to read in all probabilty maps, visit each voxel and compare the probabilities in the voxel for all structures. Generating such scrisp, winner-takes-all label maps is not recommended to calculate e.g., volumes etc, though... Hope this helps, Koen On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu bmohan.bo...@gmail.com wrote: I have completed the segmentation of hippocampal subfileds, but now I would like to know the generated images are in probability map or label map? If they are in label map what would be the best upper and lower thresholds to generate the ROI mask images. Could you please also tell me the way to do so. -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202 ___ 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] selxavg-sess outputs
Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40. -prestim 0 -polyfit 2 -TER 2. -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang ___ 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] Modifying Regression Analysis
Oh, sorry, I had misunderstood your question. Yes, you will need to create a new paradigm file and a new analysis to go with it. The actual analysis should not take that much time because all the preprocessing is already done. It will probably take 15-20 min per subject. doug Adam Nitenson wrote: I'm not sure how I could do that considering that, in the paradigm file, the 1, 3, 5, and 7 loads are all designated with the same condition number (2), while the weight is what varies. My current contrast (2vFix) encompassed all four loads so I'm not sure how I could just make a new contrast without altering the condition number for the 7-load, and thus requiring a new analysis. -Adam Hi Adam, why not just make a new contrast with 1, 3, and 5? You can then run selxavg3-sess -- it will recognized that you only added a contrast and just re-run the contrast (should be pretty quick). doug Adam Nitenson wrote: Hi Doug and Freesurfers, I am currently analyzing data acquired from the Sternberg memory task, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single contrast. My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data. From looking at the analysis setup, it looks like I would have to make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the 2s in the paradigm file to 1s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially ignore the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg-sess outputs
Hi Doug, Thank you for prompt reply. So I should remove '-gammafit', and add '-fir 4 24' is for mkanalysis-sess.new? Yang On Tue, Aug 9, 2011 at 11:42 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: If you want a time course, you should use an FIR model, something like -fir 4 24 to start the time window 4 sec before the stimulus onset and stop it 20 sec after stimulus onset. Do not include -gammafit. doug Yang Liu wrote: Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40. -prestim 0 -polyfit 2 -TER 2. -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**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. ___ 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] selxavg-sess outputs
Yes, but don't use mkanalysis-sess.new. Are you not using version 5.X? doug Yang Liu wrote: Hi Doug, Thank you for prompt reply. So I should remove '-gammafit', and add '-fir 4 24' is for mkanalysis-sess.new? Yang On Tue, Aug 9, 2011 at 11:42 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If you want a time course, you should use an FIR model, something like -fir 4 24 to start the time window 4 sec before the stimulus onset and stop it 20 sec after stimulus onset. Do not include -gammafit. doug Yang Liu wrote: Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40. -prestim 0 -polyfit 2 -TER 2. -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selxavg-sess outputs
After I run recon-all -version, it shows: v 1.133.2.57 2009/08/06'. Since we have a lot of scripts for the older version, we kept using the old one. If we don't use mkanalysis-sess.new, what we shall use? Yang On Tue, Aug 9, 2011 at 12:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Yes, but don't use mkanalysis-sess.new. Are you not using version 5.X? doug Yang Liu wrote: Hi Doug, Thank you for prompt reply. So I should remove '-gammafit', and add '-fir 4 24' is for mkanalysis-sess.new? Yang On Tue, Aug 9, 2011 at 11:42 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: If you want a time course, you should use an FIR model, something like -fir 4 24 to start the time window 4 sec before the stimulus onset and stop it 20 sec after stimulus onset. Do not include -gammafit. doug Yang Liu wrote: Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40. -prestim 0 -polyfit 2 -TER 2. -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**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. -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg-sess outputs
You're using a fairly old version of freesurfer. If you have to use this, then use mkanalysis-sess (without the .new). doug Yang Liu wrote: After I run recon-all -version, it shows: v 1.133.2.57 2009/08/06'. Since we have a lot of scripts for the older version, we kept using the old one. If we don't use mkanalysis-sess.new, what we shall use? Yang On Tue, Aug 9, 2011 at 12:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yes, but don't use mkanalysis-sess.new. Are you not using version 5.X? doug Yang Liu wrote: Hi Doug, Thank you for prompt reply. So I should remove '-gammafit', and add '-fir 4 24' is for mkanalysis-sess.new? Yang On Tue, Aug 9, 2011 at 11:42 AM, 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 wrote: If you want a time course, you should use an FIR model, something like -fir 4 24 to start the time window 4 sec before the stimulus onset and stop it 20 sec after stimulus onset. Do not include -gammafit. doug Yang Liu wrote: Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40. -prestim 0 -polyfit 2 -TER 2. -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang ___ 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 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] Code changes to use Compiled Matlab?
Mathworks loves their parallel toolbox. We love using Condor.
I won't go into the reasons.
http://www.cs.wisc.edu/condor/
We have negotiated an unlimited license of for Matlab and I have freesurfer
recon-all broken into the three phases. This gives us currently 1700
dedicated cores
where we can process brain scans for groups on the Madison, WI campus.
We are contractually prevented from running anything but compiled Matlab
on any cluster on the UW-Madison campus.
I have had to modify mris_computer_lgi to call compiled matlab entry
points
after setting up a Matlab runtime within the Freesurfer 5.1.0 staged
executable.
What I ran into was a type mismatch from the way I now call the matlab
functionality.
Is there a known solution for this or do I have to change the matlab
entry points
to do initial type changing?
We are working on a work flow to not only process the brains but also do
FSL and matlab post processing at the same time and/or take preprocessed
subjects and do either FSL or Matlab processing.
I automate researchers on campus and don't actually program Matlab
though I can work my way through this. As a computer Scientist I don't
really want to be changing the code base in an unmanaged way.
*Change
in call
#
# make_outer_surface.m
#
# create the outer surface from the filled volume
set MLF = /tmp/mos_$$_.m
set arg1 = ${tmpdir}/${input}.filled.mgz
set arg2 = ${closespheresize}
set arg3 = ${tmpdir}/${input}-outer
rm -f ${arg3}
# bt commented out for converting to compiled
echo Calling compiled matlab make_outer_surface
echo make_outer_surface('${arg1}',${arg2},'${arg3}')
make_outer_surface ${arg1} ${arg2} ${arg3}
#echo make_outer_surface('${arg1}',${arg2},'${arg3}'); exit $MLF
#echo =
#echo `cat $MLF`
#echo =
#if ($RunIt) then
#cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash
#endif
*
ERROR BELOW
Calling compiled matlab make_outer_surface
reading filled volume...
closing volume...
??? Error using == iptcheckinput
Function STREL expected its second input, R,
to be one of these types:
double
Instead its type was char.
Error in == strelParseInputs at 1308
Error in == strelstrel.strel at 143
Error in == make_outer_surface at 41
^G
Images:strel:invalidType
*
--
Bill Taylor 608-263-2656 (cell 608-219-4430)
Center for High Throughput Computing(CHTC)
Condor project
Computer Sciences
University of Wisconsin, Madison
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[Freesurfer] Functional Data Hippocampus
Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel ___ 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] Functional Data Hippocampus
Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel ___ 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] Functional Data Hippocampus
Sunil, can you elaborate on what you need? slices defined how? In the functional in the volume? doug Sunil Patel wrote: Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_watershed for generating scalp surfaces
Hello Everyone, I have an application outside freesurfer where I need the scalp/face surface from the MRI file so I'm trying to use mri_watershed algorithm to generate the scalp surface, but when I read the subject-outer_skin.surf file in matlab using the read_surf command I see that the facial features (nose, eyes, lips, chin) are not clear. But when I viewed the MRI file using mrilab I can see the facial features clearly. So I was wondering if there are parameters I can change while running the mri_watershed alrgorithm so that I can get good face shape. I'm also up for any suggestions/hints. Here is the command I used to run the mri_watershed: mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject /../..subject/T1.mgz /../../bem/watershed/ws/ Thanks and Regards, --- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 --- ___ 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] mri_watershed for generating scalp surfaces
You can try using mkheadsurf. Run it with --help to get more info. doug Vema Krishnamurthy, Santosh wrote: Hello Everyone, I have an application outside freesurfer where I need the scalp/face surface from the MRI file so I'm trying to use mri_watershed algorithm to generate the scalp surface, but when I read the subject-outer_skin.surf file in matlab using the read_surf command I see that the facial features (nose, eyes, lips, chin) are not clear. But when I viewed the MRI file using mrilab I can see the facial features clearly. So I was wondering if there are parameters I can change while running the mri_watershed alrgorithm so that I can get good face shape. I'm also up for any suggestions/hints. Here is the command I used to run the mri_watershed: mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject /../..subject/T1.mgz /../../bem/watershed/ws/ Thanks and Regards, --- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit .nii files
Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks! ___ 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] mri_glmfit .nii files
This is controlled by the $FSF_OUTPUT_FORMAT. By default this is compressed nifti (nii.gz). Both nii and nii.gz store the same information. The nii.gz is compressed, so you save some space. doug Chindhuri Selvadurai wrote: Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Functional Data Hippocampus
register your functional data to your T1, extract a hippocampus label from the aseg.mgz and apply the registration matrix to it using mri_convert to map it back to the functional space and use the mapped label to extract. cheers Bruce On Tue, 9 Aug 2011, Sunil Patel wrote: Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel ___ 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] FMRI Hemispheric Asymmetry Analyses
Hello-
I would like to directly compare asymmetries in FMRI activation in
surface space based on the Greve et al pipeline presented at HBM this year.
All of our anatomical data have been processed with FS v4.5, but the FMRI
data is in AFNI volumes. I am very new to the freesurfer program so any
corrections on how to achieve cross-hemisphere registrations would
be greatly appreciated.
1) We transformed the functional data to anatomical space using
bbregister.
2) We then registered each subject’s T1 data to the contralateral
hemisphere of fsaverage and made templates of the contra (?h.con.sphere.reg
) and ipsilateral (?h.sphere.reg ) registrations
Registration step
mris_register -curv surf/rh.sphere
{$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif
surf/rh.CON.sphere.reg
mris_register -curv surf/lh.sphere
{$FREESURFER_HOME}/average/rh.average.curvature.filled.buckner40.tif
surf/lh.CON.sphere.reg
template step
make_average_subject --out CON_TEMPLATES --surf-reg CON.sphere.reg
--subjects M87150222_20110311 M87138477_20080429 ..
make_average_subject --out IPS_TEMPLATES --surf-reg sphere.reg --subjects
M87150222_20110311 M87138477_20080429 ..
3) I then re-registered RH data to the new contralateral template
(study-specific) and LH data to the new ipsilateral template to get
everything in the same sphere space
mris_register -curv surf/rh.sphere CON_TEMPLATES/rh.reg.template.tif
surf/rh.finalTEM.sphere.reg
mris_register -curv surf/lh.sphere IPS_TEMPLATES/lh.reg.template.tif
surf/lh.finalTEM.sphere.reg
4) Finally, I apply the final registration template to aux data
(thickness, FMRI) to bring everything into a common space that can be
directly tested for hemispheric asymmetries
mris_preproc --hemi rh --target CON_TEMPLATES --surfreg finalTEM.sphere.reg
--meas thickness --out final.thickness.nii --s ${subject}
mris_preproc --hemi lh --target IPS_TEMPLATES --surfreg finalTEM.sphere.reg
--meas thickness --out final.thickness.nii --s ${subject}
Please let me if this pipeline makes sense and follows what was
proposed at the HBM meeting. Also are the iterations mentioned in the poster
necessary (ie make additional templates and re-reregister) when the sample
is relatively large (N = 100)?
Thanks!
Andrew
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Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection
Eek, that looks awful! Can you upload this subject so we can figure out what is going on? On Aug 9, 2011, at 4:09 PM, Christopher Luna cdl...@mit.edu wrote: Hello, On this topic again, we tried fixing the coordinate system (we flipped A/P) as much as we could until we heard back from our colleagues. And we also altered the white matter thresholds from mri_segment in case the missing white matter was due to some strange qualities in the original IMG files. Unfortunately, this didn't work. I've attached some example pictures of what we end up with even after tinkering with the white threshold. Are we going to have to add in this missing white matter by hand? Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 3:04 PM, Christopher Luna cdl...@mit.edu wrote: Hi Bruce, Thank you very much! We'll get in contact with them. Best, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 2:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Chris, they are front/back reversed (a/p), which is why everything fails. I don't know how you are ever going to know left from right though. You should talk to whoever got you this data and see if they have some way to tell. cheers Bruce On Mon, 1 Aug 2011, Christopher Luna wrote: I've uploaded the IMG and HDR files, they are named after my email address. Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange?highlight=%28ftp%29 On Mon, 1 Aug 2011, Christopher Luna wrote: Ah, I forgot about the left/right orientation. Where should I upload these files? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: how do you know left/right is correct? In any case, if you upload the subject we'll take a look. Things very rarely fail that badly On Mon, 1 Aug 2011, Christopher Luna wrote: Hi Bruce, The orientations are correct - they weren't at first so I had to do a lot of work in tkregister2 to get the orientations correct. Unfortunately I only have access to the *.IMG and sometimes the *.HDR file for each subject. Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Christopher, are you sure that the orientations are correct? That is, when you bring the orig.mgz up in tkmedit does the coronal view actually show the brain coronally? Img is a dangerous format to use as it doesn't contain orientation info. Do you have access to the data in some other format before it was convered to img? Bruce On Mon, 1 Aug 2011, Christopher Luna wrote: Hello Freesurfers, I'm putting *.IMG files into the program and after correcting talaraich transformations for them, I notice that when the reconstructions have completed, that there are entire lobes of white matter absent from the surfaces detected and from the wm.mgz file. I went through my hand at first to manually fill in the missing white matter for the first case, but after seeing how many were affected, I figured there was some setting I may be missing or some contrast level that may be off. I had tried using control points, but after following the WIKI instructions on regenerating surfaces after placing them, I found no significant difference in white matter detection. How do I ensure all of the white matter in my converted IMGs is identified? Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT 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
