[Freesurfer] TRACULA question: pathstats.overall.txt
Dear TRACULA Developer & User, I am wondering if it is possible to add other DTI measurements to the pathstats.overall.txt along with those DTI parameters already included (FA, MD, AD, RD)? Thank you very much. Minjie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal segmentation doubts
Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the "kvlQuantifyHippocampalSubfieldSegmentations.sh" I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissurec_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is "0.5*0.5*0.5mm^3". Many thanks in advanced,Gabriel -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] Corrections in Skull Stripping lead to changes in aseg.stats - underlying reasons
Hello, After making some corrections to the skull stripping (by hand) and running recon-all I was really puzzled to notice that there had been changes in the aseg.stats. Here are the statistics: # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 222913.677586, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 223162.652586, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 446076.330172, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 197877.640625, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 199335.75, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 397213.390625, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 172184.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 618260.330172, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 976560.279689, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1340641.214487, mm^3 -- # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 221898.779029, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 221558.440924, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 443457.219953, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 196538.375000, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 199342.906250, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 395881.281250, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 172740.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 616197.219953, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 974785.433550, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1340641.214487, mm^3 -- As you can see only the ICV stays the same but everything else changes: How can this be? Thank you very much for your answer in advance! Regards Thomas ___ 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] Recent paper on FreeSurfer reliability
Dear Bruce, Doug, Nick, and other co-workers, As authors of the recent paper “The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements” we would like to take the opportunity to respond to the numerous e-mails and reactions written on mailings lists and websites. We have never expected that our paper would have such an adverse impact. We have noticed that several so-called “journalists” have misinterpreted and erroneously extrapolated our conclusions. Even though this is not in our hands, we want to express our disappointment of these events and that we feel very uncomfortable with the created harassment. We want to stress that it has never been our intention to put FreeSurfer in a bad light or to blame its developers, rather we wanted to quantify the effects that you frequently warned the users about. The results of our study confirm your recommendations and increase the awareness of such effects to (novice) users. It is of course unavoidable that modifications to algorithms will produce different results; we, nevertheless, must admit that we were surprised that some effects were rather large. We are using FreeSurfer frequently for our MRI data and we definitely intend to do so in the future. We are impressed by the efforts of your team to improve the algorithms and to extend the capabilities of FreeSurfer. We are most grateful to you and the other developers because these continuing efforts enabled and will enable us to perform our research in a valid and proper manner. Unfortunately, the media attention gave the impression that our conclusions would only be directed to FreeSurfer. We have written in our discussion section that some of the conclusions may apply to other packages in the field of neuroimaging as well. We hope that you can acknowledge our sincere intention to examine and increase awareness of uncontrolled variation in MRI data analyses in general and not to pinpoint Freesurfer. Therefore, we have informed also the users and developers of FSL about possible similar effects. Ed Gronenschild, Petra Habets, Heidi Jacobs, Ron Mengelers, Nico Rozendaal, Jim van Os, Machteld Marcelis ___ 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] TRACULA question: pathstats.overall.txt
Hi Minjie - These commonly used measures are provided for your convenience. You can always use the reconstructed path distribution volume path.pd.nii.gz, thresholded or not, as a mask to average your measurement of choice. a.y On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear TRACULA Developer & User, > > I am wondering if it is possible to add other DTI measurements to the > pathstats.overall.txt along with those DTI parameters already included > (FA, MD, AD, RD)? > > Thank you very much. > Minjie > ___ > 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] TRACULA question: pathstats.overall.txt
Dear Dr. Yendiki, Thank you very much for your quick response. To calculate the weighted DTI measure, per your previous emails, we would need to normalize path.pd.nii.gz, right? If this is the case, we could use the following equation correct for weighted measurement: dti_para (DTI parameter image) path_pd (path.pd.nii.gz) sum(dti_para.*path_pd))/sum(path_pd) Thank you very much. Minjie On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki wrote: > > Hi Minjie - These commonly used measures are provided for your convenience. > You can always use the reconstructed path distribution volume > path.pd.nii.gz, thresholded or not, as a mask to average your measurement of > choice. > > a.y > > > On Thu, 28 Jun 2012, Minjie Wu wrote: > >> Dear TRACULA Developer & User, >> >> I am wondering if it is possible to add other DTI measurements to the >> pathstats.overall.txt along with those DTI parameters already included >> (FA, MD, AD, RD)? >> >> Thank you very much. >> Minjie >> ___ >> 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] lh.pial question
Hi all, Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few vertices we think are causing errors for a 3D printing we are trying to do. Thanks, m ___ 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] TRACULA question: pathstats.overall.txt
Yes, if you wanted to do a weighted average of your measure. Or you could just theshold and binarize path.pd and use it a simple ROI to do an unweighted average. On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear Dr. Yendiki, > > Thank you very much for your quick response. To calculate the weighted > DTI measure, per your previous emails, we would need to normalize > path.pd.nii.gz, right? If this is the case, we could use the following > equation correct for weighted measurement: > > dti_para (DTI parameter image) > path_pd (path.pd.nii.gz) > > sum(dti_para.*path_pd))/sum(path_pd) > > Thank you very much. > > Minjie > > > > > On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki > wrote: >> >> Hi Minjie - These commonly used measures are provided for your convenience. >> You can always use the reconstructed path distribution volume >> path.pd.nii.gz, thresholded or not, as a mask to average your measurement of >> choice. >> >> a.y >> >> >> On Thu, 28 Jun 2012, Minjie Wu wrote: >> >>> Dear TRACULA Developer & User, >>> >>> I am wondering if it is possible to add other DTI measurements to the >>> pathstats.overall.txt along with those DTI parameters already included >>> (FA, MD, AD, RD)? >>> >>> Thank you very much. >>> Minjie >>> ___ >>> 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] Building ROI from SPM5 MNI results
Hi Everyone, I would like to "import" an ROI into a FS analysis and extract thickness measures form within this region. Is this at all possible? Thanks Anson K, ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ 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] TRACULA question: pathstats.overall.txt
Thank you very much. We would like to do the weighted measure, as we believe it would be more sensitive and robust to WM abnormalities in our patient population. Minjie On Thu, Jun 28, 2012 at 11:52 AM, Anastasia Yendiki wrote: > > Yes, if you wanted to do a weighted average of your measure. Or you could > just theshold and binarize path.pd and use it a simple ROI to do an > unweighted average. > > > On Thu, 28 Jun 2012, Minjie Wu wrote: > >> Dear Dr. Yendiki, >> >> Thank you very much for your quick response. To calculate the weighted >> DTI measure, per your previous emails, we would need to normalize >> path.pd.nii.gz, right? If this is the case, we could use the following >> equation correct for weighted measurement: >> >> dti_para (DTI parameter image) >> path_pd (path.pd.nii.gz) >> >> sum(dti_para.*path_pd))/sum(path_pd) >> >> Thank you very much. >> >> Minjie >> >> >> >> >> On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki >> wrote: >>> >>> >>> Hi Minjie - These commonly used measures are provided for your >>> convenience. >>> You can always use the reconstructed path distribution volume >>> path.pd.nii.gz, thresholded or not, as a mask to average your measurement >>> of >>> choice. >>> >>> a.y >>> >>> >>> On Thu, 28 Jun 2012, Minjie Wu wrote: >>> Dear TRACULA Developer & User, I am wondering if it is possible to add other DTI measurements to the pathstats.overall.txt along with those DTI parameters already included (FA, MD, AD, RD)? Thank you very much. Minjie ___ 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] Pial and WM boundary edits
To whom it may concern, After running autorecon2 (recon-all -subjid -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File > Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File > Save Volume. After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid ) however received an error that '-autorecon-pial' was not recognized. Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler -- Skyler G. Shollenbarger Graduate Student Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee ___ 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] lh.pial question
you could create a patch by cutting them out in tksurfer On Thu, 28 Jun 2012, Borzello, Mia wrote: > Hi all, > > Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few > vertices we think are causing errors for a 3D printing we are trying to do. > > Thanks, > m > > ___ > 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] Pial and WM boundary edits
Hi Skyler after adding control points one usually runs: recon-all -subjid -autorecon2-cp -autorecon3 cheers Bruce On Thu, 28 Jun 2012, Skyler Gabriel Shollenbarger wrote: > To whom it may concern, > > After running autorecon2 (recon-all -subjid -autorecon2) there were > areas that required correcting for both the pial and WM boundaries. > I added control points to correct the WM boundaries and saved them using File > > Save Control Points. I also used the select voxels tool to extend the > boundaries in areas where the pial surface was not generous enough resulting > in excluded GM and saved them using File > Save Volume. > > After adding these voxels and control points I ran (recon-all -autorecon-pial > -subjid ) however received an error that '-autorecon-pial' was not > recognized. > > Then, in attempt to regenerate the boundaries with the new voxels and control > points saved, I ran (recon-all -subjid -autorecon2-cp). > When reloading the image to inspect the new boundaries using command (tkmedit > brainmask.mgz -surfs -segmentation wm.mgz > $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. > > If anyone has insight into what I'm doing incorrectly it would be much > appreciated! > Skyler > > ___ 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_robust_template- Segmentation Fault
Hi there Freesurfer, I am running into a seg fault while running mri_robust_template on freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build. Thinking that this may perhaps be an OS-related issue, I tried to download FS binaries from http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/ but the link is dead Any help would be appreciated Usman $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --satit: Will estimate SAT iteratively! --mov: Using 191_0001.nii.gz as movable/source volume. --mov: Using 192_0001.nii.gz as movable/source volume. Total: 2 input volumes --template: Using test.nii.gz as template output volume. reading source '191_0001.nii.gz'... reading source '192_0001.nii.gz'... Segmentation fault (core dumped) ___ 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_robust_template- Segmentation Fault
The link works for me. You can also try ftp instead of http. Best, Martin On Thu, 2012-06-28 at 14:41 -0400, Usman Khan wrote: > Hi there Freesurfer, > I am running into a seg fault while running mri_robust_template on > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 > build. > > > Thinking that this may perhaps be an OS-related issue, I tried to > download FS binaries > from http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/ > but the link is dead > > > Any help would be appreciated > > > Usman > > > $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ > > > --satit: Will estimate SAT iteratively! > --mov: Using 191_0001.nii.gz as movable/source volume. > --mov: Using 192_0001.nii.gz as movable/source volume. > Total: 2 input volumes > --template: Using test.nii.gz as template output volume. > reading source '191_0001.nii.gz'... > reading source '192_0001.nii.gz'... > Segmentation fault (core dumped) > > > > ___ > 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.
