[Freesurfer] TkmEdit Scripting SetBrushInfo Error
Hi, I am getting tzhe following an error if I use the following command in a tcl-script: SetBrushInfo 3 1 2000 1 The error is: Error: Parsing script file This error was encountered while running the script specified with the -tcl option. What is wrong? Sincerely yours pfannmoe ___ 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] One sample t-test in Qdec
Hello, I would like to learn whether we can conduct one-sample t-test using Qdec. I'm working on a single-case study, and I want to compare a single subject's data with a group of controls (to see how this specific subject is different from the group) in terms of volume, thickness and meancurvature. As far as I know, we can do the analysis in Terminal, but I would like to see have the brain figure output (cluster by cluster) in Qdec for one sample t-test as well. Is it possible? Thanks in advance, Buse. ___ 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] Combining sagittal and axial T1 for volumetric analysis
I have patients and controls scanned on the same scanner but their data was acquired in different orientations. One group is sagittal and the other is axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images for freesurfer analysis? Thanks carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. ___ 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] Combining sagittal and axial T1 for volumetric analysis
Hi Carmela are all controls scanned with one protocol and all patients with another? If so, combining them and interpreting the results is going to be difficult. sorry Bruce On Wed, 5 Mar 2014, Tartaglia, Carmela wrote: I have patients and controls scanned on the same scanner but their data was acquired in different orientations. One group is sagittal and the other is axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images for freesurfer analysis? Thanks carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. ___ 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] Is there a better direction for acquiring T1 structural scan? sagittal or axial
I am wondering if there is a preferred direction for acquiring T1 structural scan? sagittal or axial? and what is the rational? Thanks Carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. ___ 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] different thickness after converting wm.mgz in nifti and back
Hi Karl why is there any difference in either geometry or pixel values after converting back and forth? Can you send us your mri_convert command lines and screen output? cheers Bruce On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschut...@uni-graz.at) wrote: Dear experts, our group decided to make all the white matter edits in brainvoyager (don't ask me why;-). So we converted the wm.mgz into nii and then into the brainvoyager format vmr, made the edits and the same way back into freesurfer. We started the recon-all -autorecon2-wm … and found massive reduction in the thickness. So far so bad. To figure out the problem we started at the beginning of the conversion-mess and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the same reduction in the thickness. Finally, here comes my question. Is it possible that due to interpolation errors in the mri_convert routine this reduction can be explained? PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: Volumes differ in geometry row=1 col=1 diff=0.00 (5.96046e-08) Please fin attached the reconstructed white matter surface (red = original, yellow = after converting the wm from nii in mgz and back) thank you so much best Karl___ 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] Qdec failed
Dear experts, I have Freesurfer running quite well on Ubuntu for some time. But today when I tried to run the command ‘qdec’, I got the following error: Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory How do I fix this? Thank you. Yinfei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10
Thank you for the information, I wasn't sure if the centos4 build had mp built into it. I will try this and forward the information on to the researcher to see how their runs can be improved. Regards Michael weiner -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, March 04, 2014 1:17 PM To: Weiner, Michael; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10 Hello Michael, Use the Freesurfer Centos4 build for your Centos5 platform. People who want to take advantage of of multiple cores typically use the -openmp num cores flag when running recon-all. Theoretically the more cores you use the faster the runtime, but we have found that that there is little gain after 8 and when using that many we typically only see a 25% decrease in the time it takes to run the entire recon-all stream. You could try and get fancy by writing up a script and breaking up the reson-all stream into parts and parrallelizing some of the processing of the left and right hemispere... something along the lines of: recon-all -s subj -autorecon1 -openmp 8 recon-all -s subj -autorecon2-volonly -openmp 8 recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify rh-done.log -openmp 8 recon-all -s subj -autorecon2-perhemi -hemi lh -log recon-all-hemi-lh.log -notify lh-done.log -openmp 8 while (rh-done.log AND lh-done.log do not both exist) do sleep 1 end loop recon-all -s subj -autorecon3 -openmp 8 -Zeke On 03/03/2014 10:21 AM, Weiner, Michael wrote: I have recently upgraded our server from v5.0.0 to v5.3.0 running on CentOS 5.10 and was a little surprised that there wasnt a version of Freesurfer built for this platform but rather 4 and 6. I guess my main question is, was the version for centos4 built with openmpi at all? THe server we are running Freesurfer on has 48 cores and we are trying to figure out how to make sure that while running Freesurfer we take advantage of all these cores. Is there any documentation that i can look at to help me in this endeavor or does anyone have any tips they can share? Thank you in advance Michael Weiner Lead Analyst/UNIX Systems Administrator Lerner Research Institute Computing Services Lerner Research Institute Cleveland Clinic === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News World Report (2013). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News World Report (2013). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list
Re: [Freesurfer] LGI in Qdec
Hi Marie, It appears that the problem was the program that I was using to create the . Qdecrc file. I was using Text Wrangler. I switched to TextMate and the problem has been resolved. Thanks so much for your help! Krista On Tue, Mar 4, 2014 at 8:27 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Krista, Did you verify that your changes to .Qdecrc were properly saved? As long as the command more ~/.Qdecrc doesn't give you a line with MEASURE1 = pial_lgi, then you'll not have it in qdec menu. And version should not be an issue. How do you edit the .Qdecrc file? Did you check to see whether opening qdec had any effect on the line that you added (by running the command more ~/.Qdecrc before and after opening qdec)? I need you to explain me a bit more how you did, otherwise it's difficult for me to help you. Marie On Mar 4, 2014, at 5:20 PM, krista kelly krista.kell...@gmail.com wrote: Hi Marie, Thanks for the the response. I've done that a few times and still, the lgi option does not come up in qdec as a measure. Could it be that I'm using an outdated version of Qdec? My freesurfer v is 5.3 so unless I need to update qdec on its own, I don't think that this is the problem. Any other ideas? Best, Krista On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer marie.sch...@unige.chwrote: Hi Krista, You need to add the following line in your .Qdecrc: MEASURE1 = pial_lgi and save the change. I don't think it matters where you add it, I have it before all the Qdec lines. Then start qdec again, it should work. If not, check again the .Qdecrc file, and look whether starting qdec erases the added line. Let me know, Marie On Feb 28, 2014, at 1:09 PM, krista kelly krista.kell...@gmail.com wrote: Hi Marie, The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here is the output when I run more ~/.Qdecrc: # This file is automatically generated by the application # If you change any lines or add new lines, note that all # coments and empty lines will be deleted. Every line has # to be in format: # key = value # Qdec1\Dialogs\ExitApplication = 0 Qdec1\Dialogs\SendErrorLog = 0 Qdec1\Geometry\MainPanelSize = 375 Qdec1\Geometry\MainPanelVisibility = 1 Qdec1\Geometry\SaveUserInterfaceGeometry = 1 Qdec1\Geometry\SecondaryPanelSize = 250 Qdec1\Geometry\SecondaryPanelVisibility = 0 Qdec1\Geometry\ViewPanelPosition = Right Qdec1\Geometry\WindowGeometry = 900x700+787+1 Qdec1\MRU\File00 = /Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat Qdec1\MRU\File00Cmd = LoadDataTable Qdec1\RunTime\MostRecentVersionLaunched = 1.4 Qdec1\RunTime\PrintTargetDPI = 100.00 Qdec1\RunTime\ShowBalloonHelp = 1 Qdec1\RunTime\ShowSplashScreen = 1 Qdec1\RunTime\ToolbarFlatButtons = 1 Qdec1\RunTime\ToolbarFlatFrame = 1 Thanks! Krista On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer marie.sch...@unige.chwrote: Hi Krista, Can you please run: more ~/.Qdecrc and copy paste the output for me? The rm: No match issue in the qcache is not a problem, it's independent from the issue of listing lGI in the qdec menu. Even with the no match output in the qcache command, all the files should have been created properly (you can check that you have some files named ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject if you want to be sure. Let me know, Marie On Feb 25, 2014, at 6:55 PM, krista kelly krista.kell...@gmail.com wrote: Hi Marie, I have tried adding the .Qdecrc file into the home folder as well but that does not work. The lgi measure is not appearing in the dropdown menu in the design tab in Qdec. Further, when I ran recon-all -qcache -measure pial_lgi, there were error messages saying 'rm: No match', although the -qcache exited without errors. Could this be the problem? If not, does anyone have any ideas? Thanks! Krista On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer marie.sch...@unige.chwrote: Hi Krista, Can you be more specific about what is not coming up? If lGI not listed in the menu of qdec, look at the following post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html Otherwise can you describe more precisely the issue? Best, Marie On Feb 24, 2014, at 1:21 PM, krista kelly krista.kell...@gmail.com wrote: Hello, I followed instructions on how to incorporate the lgi_pial measure into QDec, however, it's not coming up when I go to choose this as a measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as to why this may be occurring? Thanks, Krista ___ 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
Re: [Freesurfer] One sample t-test in Qdec
Hi Buse, I think this is a two-sample t-test where the 2nd sample is your individual. You should be able to this in qdec doug On 03/05/2014 07:52 AM, Buse Merve Ürgen wrote: Hello, I would like to learn whether we can conduct one-sample t-test using Qdec. I'm working on a single-case study, and I want to compare a single subject's data with a group of controls (to see how this specific subject is different from the group) in terms of volume, thickness and meancurvature. As far as I know, we can do the analysis in Terminal, but I would like to see have the brain figure output (cluster by cluster) in Qdec for one sample t-test as well. Is it possible? Thanks in advance, Buse. ___ 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] Freesurfer 5.3 and CentOS 5.10
Micheal, Im sorry but I sent you conflicting information. The Centos4 build does NOT have openmp built into it. Our Centos4 builds use gcc version 3.4.6. It wasnt till gcc 4.2 that the gcc compiler implement openmp (v2.5) Our CentOS6 build uses gcc 4.4.7 and does have openmp built into it. Sorry for the confusion. -Zeke On 03/05/2014 10:15 AM, Weiner, Michael wrote: Thank you for the information, I wasn't sure if the centos4 build had mp built into it. I will try this and forward the information on to the researcher to see how their runs can be improved. Regards Michael weiner -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, March 04, 2014 1:17 PM To: Weiner, Michael; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10 Hello Michael, Use the Freesurfer Centos4 build for your Centos5 platform. People who want to take advantage of of multiple cores typically use the -openmp num cores flag when running recon-all. Theoretically the more cores you use the faster the runtime, but we have found that that there is little gain after 8 and when using that many we typically only see a 25% decrease in the time it takes to run the entire recon-all stream. You could try and get fancy by writing up a script and breaking up the reson-all stream into parts and parrallelizing some of the processing of the left and right hemispere... something along the lines of: recon-all -s subj -autorecon1 -openmp 8 recon-all -s subj -autorecon2-volonly -openmp 8 recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify rh-done.log -openmp 8 recon-all -s subj -autorecon2-perhemi -hemi lh -log recon-all-hemi-lh.log -notify lh-done.log -openmp 8 while (rh-done.log AND lh-done.log do not both exist) do sleep 1 end loop recon-all -s subj -autorecon3 -openmp 8 -Zeke On 03/03/2014 10:21 AM, Weiner, Michael wrote: I have recently upgraded our server from v5.0.0 to v5.3.0 running on CentOS 5.10 and was a little surprised that there wasnt a version of Freesurfer built for this platform but rather 4 and 6. I guess my main question is, was the version for centos4 built with openmpi at all? THe server we are running Freesurfer on has 48 cores and we are trying to figure out how to make sure that while running Freesurfer we take advantage of all these cores. Is there any documentation that i can look at to help me in this endeavor or does anyone have any tips they can share? Thank you in advance Michael Weiner Lead Analyst/UNIX Systems Administrator Lerner Research Institute Computing Services Lerner Research Institute Cleveland Clinic === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News World Report (2013). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News World Report (2013). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the
Re: [Freesurfer] Freesurfer for rodents
Hi Claudia, I don't know of anyone using it for rodents. In general, it is highly tuned to the parameters of the primate (mostly human) brain, and I think it would be quite difficult to adapt it to rodents. I'm cc'ing the FS list in case someone else has anything to add. doug On 03/05/2014 03:09 AM, Falfan-Melgoza, Claudia wrote: Dear Dr. Greve, I work at the Central Institute of Mental Health in Mannheim, Germany and I am quite sure you have heard this question to no end but I would like to ask you how viable would it be to use Freesurfer for rats and mice?, I have read that providing an atlas of the rodent brain would be the first step but as a first timer attempting to use Freesurfer I am not quite sure that would cut it, or if the next steps in the pipeline would need also a good amount of modification. And one last question, do you know of other software that in your opinion could be more suitable for rodents? I appreciate greatly your time and thank you very much in advance, Claudia Falfan-Melgoza Central Institute of Mental Health J5- 68159 Mannheim, Germany -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tkmedit edit voxel tcl script
Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ 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] extract pial_lgi from v1.thresh labels
Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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] extract pial_lgi from v1.thresh labels
try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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] Problematic dilated ventricles
It contains the volumes of the white matter parcellation. You can make a table with asegstats2table and specifying --stats=wmparc.stats doug On 03/05/2014 11:16 AM, Victor Kovac wrote: So, I assume the aseg.mgz contains the values represented in the asegstats2table, but what values does the wmparc.mgz contain? Is this where the output for the aparcstats2table comes from? Thanks! Victor On Tue, Mar 4, 2014 at 9:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The wmparc is off because the surfaces are incorrect. The aseg does not have to follow the surfaces, but wmparc does doug On 03/03/2014 03:10 PM, Victor Kovac wrote: Hi Bruce and Doug, cp aseg.auto.mgz aseg.mgz was my last step before running -autorecon2-cp -autorecon3, as suggested by Bruce before, so I am not sure what the problem could be. Since there seem to be problems re-creating the pial/wm surfaces this way, would it be possible for you to send the entire subject folder to me via GoogleDrive or some other method? I also have another question: I have loaded a subject with tkmedit, but the segmentation looks drastically improved when the -segmentation is aseg.auto_noCCseg.mgz instead of -wmparc.mgz (images attached), though the pial surface does not reflect this. Could you tell me why this is? And is it possible to get the pial/wm surfaces to follow along the lines of the aseg.auto_noCCseg.mgz segmentation? I am sorry if this is a naive question. Also: the images are from the original aseg.auto_noCCseg.mgz of this subject (MPS2002-3), not the updated one you sent me, Bruce. Thank you! Victor On Mon, Mar 3, 2014 at 10:53 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: I think that it should. To be safe, I would cp aseg.auto.mgz aseg.mgz otherwise aseg.mgz will not change (any differences will be interpreted as manual changes) doug On 03/02/2014 10:07 AM, Bruce Fischl wrote: Hi Victor hmmm, I'm not sure why that didn't work. Perhaps someone else can comment? Doug or Nick: if the aseg.mgz is recreated and you start with -autorecon2-cp shouldn't it propagate the effects of the new aseg forward? cheers Bruce On Thu, 27 Feb 2014, Victor Kovac wrote: Dear Bruce, Have you had any time to try to analyze our subject MPS2002-3? I believe you mentioned you would give it a shot in your free time a couple of months ago. Also, you were kind enough to analyze a subject for me, MPS1036-1, and sent me aseg.auto_noCCseg.new.mgz. I replaced the original file and removed thee new within the title, and then, to re-create the pial and wm surfaces, I ran: set mdir=$SUBJECTS_DIR/MPS1036-1/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta MPS1036-1 cp aseg.auto.mgz aseg.mgz and then: recon-all -autorecon2-cp -autorecon3, which I believe starts the recon-all pipeline at normalization2, as you suggested. However, this has yielded no effect that I can see when I visualize the subject with tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Any advice would be greatly appreciated! Attached is the recon-all.log for this subject. Let me know if I should cc the group. Thank you. Victor On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Victor for each subject I think you want to run: set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz then run recon-all from normalization2 forward (check the recon-all -help for these
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
sorry, it is --slabel btw, there is documentation. If you run it without options it gives you a list of arguments as well as examples doug On 03/05/2014 11:32 AM, krista kelly wrote: Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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: 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
*I would use BrainSegNotVent* found in aseg.stats. You can get more info here http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats doug On 03/04/2014 10:57 AM, Hugh Pemberton wrote: Hi guys, just wondering what you'd say is the best measure for whole brain volume? Cortex volume.. Cortical white matter volume.. Total gray volume.. Intracranial volume.. etc. Cheers! Hugh ___ 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] TkmEdit Scripting SetBrushInfo Error
Allright, it works if I use those commands:
UpdateBrushInfo { inBrush inLow inHigh inNewValue inMode inCloneSource }
SetEditBrushConfiguration
___
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] extract pial_lgi from v1.thresh labels
Perfect, it works thanks! On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: sorry, it is --slabel btw, there is documentation. If you run it without options it gives you a list of arguments as well as examples doug On 03/05/2014 11:32 AM, krista kelly wrote: Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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: 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] extract pial_lgi from v1.thresh labels
Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 371, in module parc_measure_map = parsed.parse(options.meas) File /Applications/freesurfer/bin/fsutils.py, line 207, in parse val = float(strlist[self.measure_column_map[measure]]) ValueError: could not convert string to float: Seg I've attached an example of the file created during mri_segstats in case that helps. Thanks! Krista On Wed, Mar 5, 2014 at 1:21 PM, krista kelly krista.kell...@gmail.comwrote: Perfect, it works thanks! On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: sorry, it is --slabel btw, there is documentation. If you run it without options it gives you a list of arguments as well as examples doug On 03/05/2014 11:32 AM, krista kelly wrote: Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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: 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh. harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ lh.V1.thresh.label.LGI.stats Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
use asegstats2table (I know, it's confusing:) doug On 03/05/2014 01:42 PM, krista kelly wrote: Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 371, in module parc_measure_map = parsed.parse(options.meas) File /Applications/freesurfer/bin/fsutils.py, line 207, in parse val = float(strlist[self.measure_column_map[measure]]) ValueError: could not convert string to float: Seg I've attached an example of the file created during mri_segstats in case that helps. Thanks! Krista On Wed, Mar 5, 2014 at 1:21 PM, krista kelly krista.kell...@gmail.com mailto:krista.kell...@gmail.com wrote: Perfect, it works thanks! On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: sorry, it is --slabel btw, there is documentation. If you run it without options it gives you a list of arguments as well as examples doug On 03/05/2014 11:32 AM, krista kelly wrote: Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 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: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats On 03/05/2014 11:15 AM, krista kelly wrote: Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
[Freesurfer] freesurfer coordinates question
Hello, Is there any way to extract a three dimensional coordinate representation of the different brain regions (i.e., their centroids) that freesurfer is estimating the cortical thickness of? Any help is appreciated and apologies if this question has been answered before. regards, David ___ 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] extract pial_lgi from v1.thresh labels
Thanks Doug! I did that and it worked, but now here's another problem: the values that I obtained for V1, V2, and cortex for each subject are all the same. For example, BV20 left hemisphere values for V1, V2, and cortex are all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell you what I did step by step to see if you can find where I went wrong. First, I did a for loop to run mri_segstats for each participant for each label per hemisphere (here is an example of V1): foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats hit enter end hit enter for left V2 I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats hit enter end hit enter and for left cortex I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats end hit enter This is where the problem must be occurring since all files created during these commands show the same files per hemisphere. I've attached three files created during mri_segstats (left V1, V2, cortex.stats) for one participant. I've also attached files created during asegstats2table to show how all values are the same for each label for all participants (V1, V2, cortex.LGI.txt). If anyone has any insight into the problem, that would be great! Best, Krista On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: use asegstats2table (I know, it's confusing:) doug On 03/05/2014 01:42 PM, krista kelly wrote: Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1. thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 371, in module parc_measure_map = parsed.parse(options.meas) File /Applications/freesurfer/bin/fsutils.py, line 207, in parse val = float(strlist[self.measure_column_map[measure]]) ValueError: could not convert string to float: Seg I've attached an example of the file created during mri_segstats in case that helps. Thanks! Krista On Wed, Mar 5, 2014 at 1:21 PM, krista kelly krista.kell...@gmail.commailto: krista.kell...@gmail.com wrote: Perfect, it works thanks! On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: sorry, it is --slabel btw, there is documentation. If you run it without options it gives you a list of arguments as well as examples doug On 03/05/2014 11:32 AM, krista kelly wrote: Thanks Doug, but when I try this I get the following error: Option --label unknown On Wed, Mar 5, 2014 at 11:21 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: try mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi
[Freesurfer] Running Tracula on a cluster
Hello, I plan on running a batch of subjects (around 80) on a computer cluster. I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist? However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster? I have attached my dmrirc file as well as the files needed for it to run on the cluster. Thanks, Emily dmrirc.example Description: Binary data tracula-1.sbatch Description: application/shellscript tracula-1.sh Description: application/shellscript ___ 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] Running Tracula on a cluster
Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster? a.y On Wed, 5 Mar 2014, ebell...@uwm.edu wrote: Hello, I plan on running a batch of subjects (around 80) on a computer cluster. I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist? However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster? I have attached my dmrirc file as well as the files needed for it to run on the cluster. Thanks, Emily ___ 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] Running Tracula on a cluster
Hi Anastasia, We use SLURM. I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script. Thanks, Emily - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: ebell...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster? a.y On Wed, 5 Mar 2014, ebell...@uwm.edu wrote: Hello, I plan on running a batch of subjects (around 80) on a computer cluster. I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist? However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster? I have attached my dmrirc file as well as the files needed for it to run on the cluster. Thanks, Emily The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
Sorry, I gave you some bad advice. Only use --label-thresh with labels that have a statistic that is non-zero (this is the last column of the label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is non-zero in lh.V1.label). The stat is the probability that the vertex is in the label, so you can choose the threshold based on that. The lh.V1.thresh.label is for when the stat is the max for V1 relative to the other labels (eg, V2). If you select thresh=.5, you may miss places where V1 is the most likely but still less than .5. I would probably use lh.V1.thresh.label (and then do not spec --label-thresh) doug On 03/05/2014 03:40 PM, krista kelly wrote: Thanks Doug! I did that and it worked, but now here's another problem: the values that I obtained for V1, V2, and cortex for each subject are all the same. For example, BV20 left hemisphere values for V1, V2, and cortex are all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell you what I did step by step to see if you can find where I went wrong. First, I did a for loop to run mri_segstats for each participant for each label per hemisphere (here is an example of V1): foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats hit enter end hit enter for left V2 I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats hit enter end hit enter and for left cortex I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats end hit enter This is where the problem must be occurring since all files created during these commands show the same files per hemisphere. I've attached three files created during mri_segstats (left V1, V2, cortex.stats) for one participant. I've also attached files created during asegstats2table to show how all values are the same for each label for all participants (V1, V2, cortex.LGI.txt). If anyone has any insight into the problem, that would be great! Best, Krista On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: use asegstats2table (I know, it's confusing:) doug On 03/05/2014 01:42 PM, krista kelly wrote: Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 371, in module parc_measure_map = parsed.parse(options.meas) File /Applications/freesurfer/bin/fsutils.py, line 207, in parse val = float(strlist[self.measure_column_map[measure]]) ValueError: could not convert string to float: Seg I've attached an example of the file created during mri_segstats in case that helps.
[Freesurfer] Group comparisons
Hello, I have some questions on doing group comparisons with thickness, area and volume. Many thanks in advance for any help! 1) For a DOSS design with group and gender as categorical factors, I see that an interaction contrast (Is there a group-gender interaction in the mean thickness?) still exists - but what does this contrast mean, given that DOSS by definition doesn't allow for interactions? 2) it makes sense that measures such as thickness are analysed vertex-wise in QDEC, however what does it mean when the dependent variable is area or volume - measures that do not make physical sense for a single vertex but only at the level of a region consisting of *several* vertices? 3) For values extracted from atlas regions with aparcstats2table, it seems that the product of the extracted CT and area is in the same order of magnitude as the extracted volume, but never really the same or even close - why, when the volume of a region should theoretically be the product of its surface area by its thickness? Tudor ___ 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] extract pial_lgi from v1.thresh labels
Thanks Doug! That fixed it. But now I have two numbers in each file, which do I use (see also attached file)? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795 2 1 3540 2225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 0.9794 On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Sorry, I gave you some bad advice. Only use --label-thresh with labels that have a statistic that is non-zero (this is the last column of the label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is non-zero in lh.V1.label). The stat is the probability that the vertex is in the label, so you can choose the threshold based on that. The lh.V1.thresh.label is for when the stat is the max for V1 relative to the other labels (eg, V2). If you select thresh=.5, you may miss places where V1 is the most likely but still less than .5. I would probably use lh.V1.thresh.label (and then do not spec --label-thresh) doug On 03/05/2014 03:40 PM, krista kelly wrote: Thanks Doug! I did that and it worked, but now here's another problem: the values that I obtained for V1, V2, and cortex for each subject are all the same. For example, BV20 left hemisphere values for V1, V2, and cortex are all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell you what I did step by step to see if you can find where I went wrong. First, I did a for loop to run mri_segstats for each participant for each label per hemisphere (here is an example of V1): foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats hit enter end hit enter for left V2 I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats hit enter end hit enter and for left cortex I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh. cortex.LGI.stats end hit enter This is where the problem must be occurring since all files created during these commands show the same files per hemisphere. I've attached three files created during mri_segstats (left V1, V2, cortex.stats) for one participant. I've also attached files created during asegstats2table to show how all values are the same for each label for all participants (V1, V2, cortex.LGI.txt). If anyone has any insight into the problem, that would be great! Best, Krista On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: use asegstats2table (I know, it's confusing:) doug On 03/05/2014 01:42 PM, krista kelly wrote: Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 371, in module
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
Right, one more thing. add --excludeid 0 On 03/05/2014 05:59 PM, krista kelly wrote: Thanks Doug! That fixed it. But now I have two numbers in each file, which do I use (see also attached file)? ColHeadersIndex SegId NVertices Area_mm2StructName Mean StdDevMin Max Range 1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795 2 1 35402225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 0.9794 On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, I gave you some bad advice. Only use --label-thresh with labels that have a statistic that is non-zero (this is the last column of the label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is non-zero in lh.V1.label). The stat is the probability that the vertex is in the label, so you can choose the threshold based on that. The lh.V1.thresh.label is for when the stat is the max for V1 relative to the other labels (eg, V2). If you select thresh=.5, you may miss places where V1 is the most likely but still less than .5. I would probably use lh.V1.thresh.label (and then do not spec --label-thresh) doug On 03/05/2014 03:40 PM, krista kelly wrote: Thanks Doug! I did that and it worked, but now here's another problem: the values that I obtained for V1, V2, and cortex for each subject are all the same. For example, BV20 left hemisphere values for V1, V2, and cortex are all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell you what I did step by step to see if you can find where I went wrong. First, I did a for loop to run mri_segstats for each participant for each label per hemisphere (here is an example of V1): foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats hit enter end hit enter for left V2 I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats hit enter end hit enter and for left cortex I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats end hit enter This is where the problem must be occurring since all files created during these commands show the same files per hemisphere. I've attached three files created during mri_segstats (left V1, V2, cortex.stats) for one participant. I've also attached files created during asegstats2table to show how all values are the same for each label for all participants (V1, V2, cortex.LGI.txt). If anyone has any insight into the problem, that would be great! Best, Krista On Wed, Mar 5, 2014 at 1:54 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 wrote: use asegstats2table (I know, it's confusing:) doug On 03/05/2014 01:42 PM, krista kelly wrote: Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following: mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble
Re: [Freesurfer] extract pial_lgi from v1.thresh labels
not sure what you mean, those are not mutually exclusive On 03/05/2014 06:05 PM, krista kelly wrote: Ok thanks! Also, for the lh.cortex pial_lgi, should I stick to --label-thresh .5 rather than --slabel? On Wed, Mar 5, 2014 at 5:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Right, one more thing. add --excludeid 0 On 03/05/2014 05:59 PM, krista kelly wrote: Thanks Doug! That fixed it. But now I have two numbers in each file, which do I use (see also attached file)? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795 2 1 35402225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 0.9794 On Wed, Mar 5, 2014 at 5:07 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 wrote: Sorry, I gave you some bad advice. Only use --label-thresh with labels that have a statistic that is non-zero (this is the last column of the label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is non-zero in lh.V1.label). The stat is the probability that the vertex is in the label, so you can choose the threshold based on that. The lh.V1.thresh.label is for when the stat is the max for V1 relative to the other labels (eg, V2). If you select thresh=.5, you may miss places where V1 is the most likely but still less than .5. I would probably use lh.V1.thresh.label (and then do not spec --label-thresh) doug On 03/05/2014 03:40 PM, krista kelly wrote: Thanks Doug! I did that and it worked, but now here's another problem: the values that I obtained for V1, V2, and cortex for each subject are all the same. For example, BV20 left hemisphere values for V1, V2, and cortex are all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell you what I did step by step to see if you can find where I went wrong. First, I did a for loop to run mri_segstats for each participant for each label per hemisphere (here is an example of V1): foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats hit enter end hit enter for left V2 I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats hit enter end hit enter and for left cortex I ran: foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) hit enter mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats end hit enter This is where the problem must be occurring since all files created during these commands show the same files per hemisphere. I've attached three files created during mri_segstats (left V1, V2, cortex.stats) for one participant. I've also attached files created
[Freesurfer] Surface area in aparc stats
Hi all, I need to know how is the SurfArea in ?h.aparc.stats calculated by FreeSurfer? Since each cortical parcellation has its own thickness in 3D space, does the surface area computation consider both the exterior surface (i.e. the surface separating the gray matter and the background) and the interior surface (i.e. the surface separating the gray matter and the white matter)? Thanks! Zhuangming Shen ___ 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] Surface area in aparc stats
By default, the surface area is computed from the white surface (ie, boundary between WM and GM). It is possible to compute it from the pial surface (ie, boundary between GM and background) doug On 3/5/14 9:14 PM, ??? wrote: Hi all, I need to know how is the SurfArea in ?h.aparc.stats calculated by FreeSurfer? Since each cortical parcellation has its own thickness in 3D space, does the surface area computation consider both the exterior surface (i.e. the surface separating the gray matter and the background) and the interior surface (i.e. the surface separating the gray matter and the white matter)? Thanks! Zhuangming Shen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Group comparisons
On 3/5/14 5:25 PM, Tudor Popescu wrote: Hello, I have some questions on doing group comparisons with thickness, area and volume. Many thanks in advance for any help! 1) For a DOSS design with group and gender as categorical factors, I see that an interaction contrast (Is there a group-gender interaction in the mean thickness?) still exists - but what does this contrast mean, given that DOSS by definition doesn't allow for interactions? Are you using QDEC? If so, don't use the DOSS as the contrasts are incorrect. It is possible to have an interaction among the categorical factors with a DOSS. 2) it makes sense that measures such as thickness are analysed vertex-wise in QDEC, however what does it mean when the dependent variable is area or volume - measures that do not make physical sense for a single vertex but only at the level of a region consisting of *several* vertices? The interpretation is a little more difficult. Each vertex is assigned an area equal to the average of the triangles adjacent to it. This is just a value that can be mapped to a common space like any other value (eg, thickness) (but there is a special jacobain correction to account for stretching or compression). Smoothing reduces the effect of having different sized triangles. One can think of it like this: in the common space (fsaverage) image having a patch of a certain size. When you mapped that patch back to each individual, how big would that patch be? You could then do group statistics on that number. In this way you could analyze the entire hemisphere. Now imagine doing this but making the patch smaller and smaller. 3) For values extracted from atlas regions with aparcstats2table, it seems that the product of the extracted CT and area is in the same order of magnitude as the extracted volume, but never really the same or even close -- why, when the volume of a region should theoretically be the product of its surface area by its thickness? It is an issue of how it is computed. Sum(CT*Area) != Sum(CT)*Sum(Area). When computing volume, CT*Area is computed for each vertex then summed across vertices. doug Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Surface area in aparc stats
Hi Zhuangming, please remember to post to the list. Thanks! I don't understand your question. What do you mean by the exterior, anterior, posterior, etc, surfaces? On 3/5/14 11:56 PM, 沈庄明 wrote: Hi Doug, Thank you for your prompting response. Do you mean the computation only calculate exterior surface of the cortical region ? The other five surface (i.e. anterior, posterior, left, right, interior) are excluded ? Thanks! Zhuangming -原始邮件- *发件人:* Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *发送时间:* 2014年3月6日 星期四 *收件人:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *抄送:* *主题:* Re: [Freesurfer] Surface area in aparc stats By default, the surface area is computed from the white surface (ie, boundary between WM and GM). It is possible to compute it from the pial surface (ie, boundary between GM and background) doug On 3/5/14 9:14 PM, 沈庄明 wrote: Hi all, I need to know how is the SurfArea in ?h.aparc.stats calculated by FreeSurfer? Since each cortical parcellation has its own thickness in 3D space, does the surface area computation consider both the exterior surface (i.e. the surface separating the gray matter and the background) and the interior surface (i.e. the surface separating the gray matter and the white matter)? Thanks! Zhuangming Shen ___ 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.
