Re: [Freesurfer] Subject processing difference between computers
see http://dx.plos.org/10.1371/journal.pone.0038234 On 22 Oct 2013, at 18:18, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 2 Date: Tue, 22 Oct 2013 16:15:44 + From: "West, John D." Subject: [Freesurfer] Subject processing difference between computers To: "freesurfer " Message-ID: <793d43fe7976404cb5e172709ab1f4081123f...@iu-mssg-mbx102.ads.iu.edu> Content-Type: text/plain; charset="us-ascii" Hello. We are moving our processing from an older super computer to a new one here at Indiana University. Preliminary testing is showing a significant difference between final summary stats results between subjects processed on the old system versus the new. The version of freesurfer on both systems is identical. Comparing the logs of the same subject run on both systems, I've found that the differences seem to start with the mri_watershed function specifically the main basin size. For the same subject we find: Old computer: main basin size=22667431830 voxels, voxel volume =1.000 = 22667431830 mmm3 = 22667431.936 cm3 New computer: main basin size=22208239350 voxels, voxel volume =1.000 = 22208239350 mmm3 = 22208239.616 cm3 As you can see they are very different. My theory is this is propagating through the rest of the process and giving us different summary stats at the end. I should note that both aseg and aparc stats are affected. I am also enclosing the logs for both runs as well as the differences found through the diff command (this is a lot parse through as even time stamp differences are picked up). Essentially what I am trying to find out is if these differences we are noticing are typical when changing computers and if not what could be causing these differences that I may not be picking up on. Thanks for the help. -John -- next part -- A non-text attachment was scrubbed... Name: recon-all.new.log Type: application/octet-stream Size: 451586 bytes Desc: recon-all.new.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.old.log Type: application/octet-stream Size: 450567 bytes Desc: recon-all.old.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.diff.log Type: application/octet-stream Size: 319424 bytes Desc: recon-all.diff.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment-0002.obj ___ 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] WM editing and longitudinal processing v5.3.0
Hi, From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this. FreeSurfer v5.3.0 Mac OSX10.6 Kind regards, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM editing and longitudinal processing v5.3.0
Hi Bruce, When I have a look in the recon-all script I see that it is tested if there are voxels present in wm.mgz with value 1 or 255. Both indicate wm editing. The comment in recon-all says that 1 means remove and 255 means add. And concerning my second question: are these edited voxels correcly processed with the option autorecon2-wm and subsequently with longitudinal processing? Cheers, ed On 4 Feb 2014, at 14:27, Bruce Fischl wrote: > Hi Ed, > > yes, although we reserve the values under 5 I think for editing > changes, > I believe we only use 1 at the moment. > > cheers > Bruce > On Tue, 4 Feb 2014, Ed Gronenschild > wrote: > >> Hi, >> >> From what I can read in the wiki about wm editing, I understand >> that edited wm voxels have values of either 255 (added) or >> 1 (removed) and no other values. These are stored in the file >> wm.mgz. Is that correct? >> Before processing a lot of data I want to be sure that running >> recon-all with the option autorecon2-wm will recognize these >> voxels, also during longitudinal processing. Can you confirm >> this. >> >> FreeSurfer v5.3.0 Mac OSX10.6 >> >> Kind regards, >> Ed >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM editing and longitudinal processing v5.3.0
Hi Martin, One thing I want to be sure of: should the edited wm voxels really have a value of either 1 or 255. In previous versions an added wm voxel had a value of about 110, this is not anymore the case? I'm asking this because I want to edit wm by using results from another application that segments wm, so not by means of manually editing with freeview. Cheers, Ed On 4 Feb 2014, at 17:00, Martin Reuter wrote: Hi Ed, take a look at this wiki page about edits in the long stream: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits everything should work. for long, you'd edit the base. If that is not sufficient, you can edit the cross or the long. Edits from the cross should be transferred to the long, except if the long already contain manual edits. Best, Martin On Feb 4, 2014, at 9:06 AM, Ed Gronenschild wrote: Hi Bruce, When I have a look in the recon-all script I see that it is tested if there are voxels present in wm.mgz with value 1 or 255. Both indicate wm editing. The comment in recon-all says that 1 means remove and 255 means add. And concerning my second question: are these edited voxels correcly processed with the option autorecon2-wm and subsequently with longitudinal processing? Cheers, ed On 4 Feb 2014, at 14:27, Bruce Fischl wrote: Hi Ed, yes, although we reserve the values under 5 I think for editing changes, I believe we only use 1 at the moment. cheers Bruce On Tue, 4 Feb 2014, Ed Gronenschild wrote: Hi, From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this. FreeSurfer v5.3.0 Mac OSX10.6 Kind regards, Ed ___ 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 - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Rotation involved in recon-all
Hi, Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation of the T1 data early in the pipeline, i.e., converting rawavg.mgz to orig.mgz., see excerpt of output of mri_info below rawavg.mgz: xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 : x_a = -0., y_a = -0.0066, z_a = 0.0076, c_a =14.8386 : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s =13.1335 orig.mgz: xform info: x_r = -1., y_r = -0., z_r = 0., c_r = 0.0813 : x_a = 0., y_a = -0., z_a = 1., c_a =14.8386 : x_s = 0., y_s = -1., z_s = 0., c_s =13.1335 Is that the default way of processing the data? Cheers, Ed ___ 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] Rotation involved in recon-all
Hi Bruce, Yes, I do understand that is coronal, but there is an actual rotation apart from an orientation to coronal. You can read it from the off-diagonal matrix elements. Cheers, Ed On 6 Feb 2014, at 14:36, Bruce Fischl wrote: > yes, we reorient it to be coronal as part of the "conform" process > > cheers > Bruce > On Thu, 6 > Feb 2014, Ed Gronenschild wrote: > >> Hi, >> >> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation >> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to >> orig.mgz., see excerpt of output of mri_info below >> >> rawavg.mgz: >> >> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = >> 0.0813 >> : x_a = -0., y_a = -0.0066, z_a = 0.0076, c_a = >> 14.8386 >> : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = >> 13.1335 >> >> orig.mgz: >> >> xform info: x_r = -1., y_r = -0., z_r = 0., c_r = >> 0.0813 >> : x_a = 0., y_a = -0., z_a = 1., c_a = >> 14.8386 >> : x_s = 0., y_s = -1., z_s = 0., c_s = >> 13.1335 >> >> >> Is that the default way of processing the data? >> >> Cheers, >> Ed >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Rotation involved in recon-all
Hi Harm, Thanks for the trick. Will this, however, give not rise to conversion to Talairach coordinates? Cheers, Ed On 6 Feb 2014, at 15:38, Harms, Michael wrote: > > Hi Ed, > If you want to avoid the rotation (e.g., to avoid an interpolation at the > conform step) then you need to manually alter the input so as to remove > the off-diagonal elements. That is in fact what we do as part of our > DICOM2NIFTI conversion in the HCP. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > > > > On 2/6/14 7:43 AM, "Ed Gronenschild" > wrote: > >> Hi Bruce, >> >> Yes, I do understand that is coronal, but there is an actual rotation >> apart from an orientation to coronal. >> You can read it from the off-diagonal matrix elements. >> >> Cheers, >> Ed >> >> On 6 Feb 2014, at 14:36, Bruce Fischl wrote: >> >>> yes, we reorient it to be coronal as part of the "conform" process >>> >>> cheers >>> Bruce >>> On Thu, 6 >>> Feb 2014, Ed Gronenschild wrote: >>> >>>> Hi, >>>> >>>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation >>>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to >>>> orig.mgz., see excerpt of output of mri_info below >>>> >>>> rawavg.mgz: >>>> >>>> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = >>>> 0.0813 >>>>: x_a = -0., y_a = -0.0066, z_a = 0.0076, c_a = >>>> 14.8386 >>>>: x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = >>>> 13.1335 >>>> >>>> orig.mgz: >>>> >>>> xform info: x_r = -1., y_r = -0., z_r = 0., c_r = >>>> 0.0813 >>>>: x_a = 0., y_a = -0., z_a = 1., c_a = >>>> 14.8386 >>>>: x_s = 0., y_s = -1., z_s = 0., c_s = >>>> 13.1335 >>>> >>>> >>>> Is that the default way of processing the data? >>>> >>>> Cheers, >>>> Ed >>>> >>>> >>>> ___ >>>> 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 materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3
Dear Kim, This may be of interest to you: http://dx.plos.org/10.1371/journal.pone.0038234 Cheers, Ed On 24 Mar, 2014, at 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 3 Date: Mon, 24 Mar 2014 12:28:29 +0900 From: jh kim Subject: Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3 To: Freesurfer support list Message-ID: +zv5vhvidhz3nfq...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Prof. Fischl Thanks for the valuable comments. Kim 2014-03-23 3:26 GMT+09:00 Bruce Fischl : Hi Kim we of course always strive to make things more accurate, but in the end it will depend on the details of your acquisition and such. I don't think I have a better answer than that, other than to say look at the segmentations and see if you think they are more accurate in one case than the other. sorry Bruce On Sun, 23 Mar 2014, jh kim wrote: Dear Prof. Fischl Thanks for the prompt response. The more specific reason of my query is that there was a difference in statistical significance between two FS versions. For example, the result of group comparison of left thalamic volumes (ANCOVA controlling for age and eICV) is statistically significant (p = 0.04) when using FS 5.1, whereas the result is no longer significant at all (p = 0.28) in case of FS 5.3. I'm a little confused about this discrepancy. Which result should I trust? Thank you in advance for your comments. Kim 2014-03-23 2:59 GMT+09:00 Bruce Fischl : Hi Kim there are probably lots of little reasons for the differences. This is always true for different versions, and the reason we never mix versions cheers Bruce On Sun, 23 Mar 2014, jh kim wrote: Dear FS lists When I measured subcortical GM volumes in the same subjects by using both version 5.1 and 5.3, I have observed a considerable difference in volumes between the two versions. For instance, please see the left thalamic volumes below. I cannot figure out why there is much difference between the versions. Which result is more reliable? Left-Thalamus-Proper_5.3 Left-Thalamus-Proper_5.1 10313 9757 8924.8 7746 9834.8 8287 7935.2 7034 8764.1 7747 9411.8 8037 7636.7 8051 9334.7 8255 10024.3 8171 8757.7 6900 9540.9 8316 9294.4 8369 8091 7366 9103.7 7818 9310.2 7974 7583 6872 9838.9 8911 8829.6 8004 9094.8 6973 9492.3 8922 8821.6 7691 7971.6 7376 9901.2 8936 9773.9 8855 9283.7 7615 8801.6 7690 8505.1 7325 8981 7258 9644.7 8860 9104.2 8298 8494.8 7402 9024.9 7721 8117.8 7226 8001.8 7548 8392.3 7668 8606.6 8173 9126.7 7595 8093 7885 8317.7 7157 10556 9307 8669.6 8374 8034.7 7338 8148.5 7276 9048.1 8064 8160.1 7014 8747.9 7894 8329.9 6866 8415.8 8189 9246.9 8256 8194.1 7183 9629.2 9579 7688.2 6398 8349.2 8238 8366.2 7348 8436.5 7616 8372.3 6977 9396.4 7589 9327.5 7684 10001.8 8627 9762.4 9228 8841 8532 8342.4 8024 8645.7 7725 Any comment would be appreciated. Thank you. Kim ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Convert surface to contour
Hi, When using tkmedit or freeview, a surface is converted into a contour superimposed onto T1. I would like to do the same using the command: mri_surf2vol --surf pial --hemi lh --template subjID/mri/T1.mgz \ --identity --o lh.pial.mgz --mkmask I notice that the "contour" in lh.pial.mgz is not contiguous, a lot of gaps are present. How can I obtain a nice contiguous contour? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points
Hi Bruce, I'm confused about this. The manual-intervention workflow directives listed in recon-all (6 beta) tell that the series of commands should be: -autorecon2 -autorecon2-cp -autorecon3 -autorecon2 processes stages 6-23 and -autorecon2-cp process stages 12-23 So it seems to be a waste of time to process stages 12-23 twice. My question is: how to run stages 6-23 with control points? Cheers, Ed On 26 Feb 2016, at 14:13, wrote: Hi Ed if you run the skull stripping the autorecon2 and autorecon3 it should detect and preserve your manual interventions cheers Bruce On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote: Hi, I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments? Cheers, Ed ___ 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] System crash by extremely much generated output v6 beta
Hi developers, My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full. Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
Hi Bruce, I cannot find these files in the subjects->fsaverage folder (version v5.1.0). Ed On 25 Mar 2013, at 13:58, Bruce Fischl wrote: > Hi Ed > > a combination of them (e.g. norm.mgz is used for the aseg.mz, but > brain.finalsurfs.mgz for the white/pial) > > cheers > Bruce > On Mon, 25 Mar 2013, Ed > Gronenschild wrote: > >> Hi freesurfites, >> >> The mri folder of the fsaverage subject contains >> the segmenation files, such as aparc+aseg.mgz, etc. >> and in the surf folder there the corresponding surface >> files (?h.pial. ?h.white, etc). >> Question: which T1 data was used for these >> segmentations? >> >> Cheers, >> Ed >> ___ >> 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] Recent paper on FreeSurfer reliability
Hi, The paper entitled “The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements”, PLoSONE, Vol 7(6), e38234 (2012) may be of interest to all of you. It can be found at: http://dx.plos.org/10.1371/journal.pone.0038234 Cheers, Ed ___ 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] different fs versions
Dear Marise and Laura,
As Bruce et al frequently warned users about, you should never mix
different versions.
The effects have been quantified recently by our group, see
http://dx.plos.org/10.1371/journal.pone.0038234
I can add to this that the differences between v5.1.0 and v5.0.0 are
somewhat
smaller than between v5.0.0 and v4.3.1/v4.5.0.
Cheers,
Ed
On 3 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 10
Date: Tue, 3 Jul 2012 14:32:10 +
From: "L. Koenders"
Subject: [Freesurfer] different fs versions
To: "'freesurfer@nmr.mgh.harvard.edu'"
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Dear Freesurfer people,
We attended the Freesurfer course in Amsterdam last week, thank you
so much for the information! During the course it was mentioned
that it is a very bad idea to mix Freesurfer versions during the
analysis. However, we did all the preprocessing on an external
server, using version 5.0.0 ('freesurfer-Linux-centos4_x86_64-
stable-pub-v5.0.0') and we are currently doing all of our group-
analysis on a different server, which has version 5.1.0 on it ('
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0').
Because both servers are used by a lot of people, it will become
difficult to do an update on either one of these versions. Will
this become a problem, or is there a way to avoid problems while
still using these different versions?
Thanks in advance for your help!
Kind regards,
Marise Machielsen, MD.
Laura Koenders, MSc.
Laura Koenders
PhD-student
AMC, Academic Psychiatric Centre
Department Early Psychosis
Room: PA3-138
Meibergdreef 5
1105 AZ Amsterdam
+31 (0) 20 8913 609
+31 (0) 614 285 301
www.group-project.nl
www.amcpsychiatrie-psychose.nl
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[Freesurfer] How to register FLAIR to T1?
Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to register FLAIR to T1?
Hi Bruce, It is slightly better but still displacements in all directions and rotations too exist. Ed On 10 Jul 2012, at 16:13, Bruce Fischl wrote: > try -init-spm > > cheers > Bruce > On Tue, 10 Jul 2012, Ed Gronenschild wrote: > >> Hi, >> >> I would like to register FLAIR to T1. >> Specifications FLAIR: >> axial acquisition, 24 slices, >> pixel size = 0.45 * 0.45 mm^2 >> slice thickness = 5.50 mm (no gap). >> >> The slices run from the top of the brain >> to just below the eyes. This is contrary >> to the T1 scan which covers the full head >> down to the neck. >> I have tried bbregiser as follows: >> >> bbregister --s 001 --mov 001_FLAIR.mgz \ >> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >> >> and inspected the result with >> >> tkregister2 --mov 001_FLAIR.mgz \ >> --reg 001_register.dat --surf >> >> The result looks bad, it is displaced and rotated >> by about 20 degrees with respect to T1. >> >> It makes hardly any difference if instead of --t1 >> --t2 as contrast setting was used. >> >> Is there a better way to do this registration? >> For instance, should I crop T1 to about the >> same space as covered by FLAIR? >> >> (FreeSurfer v4.5.0, MacOSX 10.5) >> >> Cheers, >> Ed >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to register FLAIR to T1?
Hi Bruce, Unfortunately, this has no effect. Ed On 10 Jul 2012, at 16:40, Bruce Fischl wrote: > Hi Ed > > you are using -t2, right? You can also try -init-header > > cheers > Bruce > On Tue, 10 Jul 2012, > Ed Gronenschild wrote: > >> Hi Bruce, >> >> It is slightly better but still displacements >> in all directions and rotations too exist. >> >> Ed >> >> On 10 Jul 2012, at 16:13, Bruce Fischl wrote: >> >>> try -init-spm >>> >>> cheers >>> Bruce >>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>> >>>> Hi, >>>> >>>> I would like to register FLAIR to T1. >>>> Specifications FLAIR: >>>> axial acquisition, 24 slices, >>>> pixel size = 0.45 * 0.45 mm^2 >>>> slice thickness = 5.50 mm (no gap). >>>> >>>> The slices run from the top of the brain >>>> to just below the eyes. This is contrary >>>> to the T1 scan which covers the full head >>>> down to the neck. >>>> I have tried bbregiser as follows: >>>> >>>> bbregister --s 001 --mov 001_FLAIR.mgz \ >>>> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >>>> >>>> and inspected the result with >>>> >>>> tkregister2 --mov 001_FLAIR.mgz \ >>>> --reg 001_register.dat --surf >>>> >>>> The result looks bad, it is displaced and rotated >>>> by about 20 degrees with respect to T1. >>>> >>>> It makes hardly any difference if instead of --t1 >>>> --t2 as contrast setting was used. >>>> >>>> Is there a better way to do this registration? >>>> For instance, should I crop T1 to about the >>>> same space as covered by FLAIR? >>>> >>>> (FreeSurfer v4.5.0, MacOSX 10.5) >>>> >>>> Cheers, >>>> Ed >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error >>> and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent >>> to you in >>> error >>> but does not contain patient information, please contact the >>> sender and >>> properly >>> dispose of the e-mail. >>> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to register FLAIR to T1?
Hi Bruce, It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions. Cheers, Ed On 10 Jul 2012, at 16:57, Bruce Fischl wrote: > Hi Ed, > > sorry, you'll have to wait until Doug is back from vacation. Is > this from > the same session? I've always had it work on flair images using one > of the > types of initialization. > > cheers > Bruce > > > On Tue, 10 Jul 2012, Ed Gronenschild wrote: > >> Hi Bruce, >> >> Unfortunately, this has no effect. >> >> Ed >> >> On 10 Jul 2012, at 16:40, Bruce Fischl wrote: >> >>> Hi Ed >>> >>> you are using -t2, right? You can also try -init-header >>> >>> cheers >>> Bruce >>> On Tue, 10 Jul 2012, >>> Ed Gronenschild wrote: >>> >>>> Hi Bruce, >>>> >>>> It is slightly better but still displacements >>>> in all directions and rotations too exist. >>>> >>>> Ed >>>> >>>> On 10 Jul 2012, at 16:13, Bruce Fischl wrote: >>>> >>>>> try -init-spm >>>>> >>>>> cheers >>>>> Bruce >>>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I would like to register FLAIR to T1. >>>>>> Specifications FLAIR: >>>>>> axial acquisition, 24 slices, >>>>>> pixel size = 0.45 * 0.45 mm^2 >>>>>> slice thickness = 5.50 mm (no gap). >>>>>> >>>>>> The slices run from the top of the brain >>>>>> to just below the eyes. This is contrary >>>>>> to the T1 scan which covers the full head >>>>>> down to the neck. >>>>>> I have tried bbregiser as follows: >>>>>> >>>>>> bbregister --s 001 --mov 001_FLAIR.mgz \ >>>>>> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >>>>>> >>>>>> and inspected the result with >>>>>> >>>>>> tkregister2 --mov 001_FLAIR.mgz \ >>>>>> --reg 001_register.dat --surf >>>>>> >>>>>> The result looks bad, it is displaced and rotated >>>>>> by about 20 degrees with respect to T1. >>>>>> >>>>>> It makes hardly any difference if instead of --t1 >>>>>> --t2 as contrast setting was used. >>>>>> >>>>>> Is there a better way to do this registration? >>>>>> For instance, should I crop T1 to about the >>>>>> same space as covered by FLAIR? >>>>>> >>>>>> (FreeSurfer v4.5.0, MacOSX 10.5) >>>>>> >>>>>> Cheers, >>>>>> Ed >>>>>> ___ >>>>>> 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] Clusterwise correction for multiple comparisons
Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to register FLAIR to T1?
Hi Doug, Thanks for your suggestion, but it didn't work out either. Ed On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 18 Date: Mon, 16 Jul 2012 11:32:06 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] How to register FLAIR to T1? To: freesurfer@nmr.mgh.harvard.edu Message-ID: <500433f6.8010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Often with FLAIR there is not enough gray-white contrast to run the registration. Try using the pial surface instead, with "-surf pial --t1" This tells it to use the pial surface as a boundary. The --t1 is needed because the intensity should go from bright to dark. Let me know if that does not fix the problem. doug On 07/10/2012 11:58 AM, Bruce Fischl wrote: glad to hear it :). You may need to repost (and possibly upload your data) On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions. Cheers, Ed On 10 Jul 2012, at 16:57, Bruce Fischl wrote: Hi Ed, sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization. cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, Unfortunately, this has no effect. Ed On 10 Jul 2012, at 16:40, Bruce Fischl wrote: Hi Ed you are using -t2, right? You can also try -init-header cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is slightly better but still displacements in all directions and rotations too exist. Ed On 10 Jul 2012, at 16:13, Bruce Fischl wrote: try -init-spm cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to register FLAIR to T1?
Hi Doug, I've found a solution to the problem: I converted T1.mgz and FLAIR.mgz to nii.gz and then applied flirt directly with the same options as in flsregister called by bbregister, so flirt -cost corratio -dof 6 -searchx -90 90 -searchy -90 90 \ -searchz -90 90 -in FLAIR.nii.gz -ref T1.nii.gz \ -out FLAIR_to_T1.nii.gz This perfectly matched the T1. Cheers, Ed On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 18 Date: Mon, 16 Jul 2012 11:32:06 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] How to register FLAIR to T1? To: freesurfer@nmr.mgh.harvard.edu Message-ID: <500433f6.8010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Often with FLAIR there is not enough gray-white contrast to run the registration. Try using the pial surface instead, with "-surf pial --t1" This tells it to use the pial surface as a boundary. The --t1 is needed because the intensity should go from bright to dark. Let me know if that does not fix the problem. doug On 07/10/2012 11:58 AM, Bruce Fischl wrote: glad to hear it :). You may need to repost (and possibly upload your data) On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions. Cheers, Ed On 10 Jul 2012, at 16:57, Bruce Fischl wrote: Hi Ed, sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization. cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, Unfortunately, this has no effect. Ed On 10 Jul 2012, at 16:40, Bruce Fischl wrote: Hi Ed you are using -t2, right? You can also try -init-header cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is slightly better but still displacements in all directions and rotations too exist. Ed On 10 Jul 2012, at 16:13, Bruce Fischl wrote: try -init-spm cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit-sim with pre-cached fails
Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed ___ 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] Fmri_glmfit-sim with pre-cached fails
Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resulting from using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 16 Date: Thu, 27 Sep 2012 11:29:06 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu Message-ID: <506470c2.5060...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking that no one would ever go above it, or maybe should never go above it. I can create tables at higher smoothing levels, but 34mm is a lot of smoothing. How much did you apply to the data? doug On 09/27/2012 05:48 AM, Ed Gronenschild wrote: Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_glmfit-sim with pre-cached fails
Doug, For the PCA residuals we found 37% for the first component. The same analysis has been done for FreeSurfer v4.5.0, and we found a residual FWHM of 15.27 and 30% for the first PCA component. The time courses showed some outliers for both versions, very much dependent on the position on the surface, i.e., each time different subjects were outside the confidence limits. Summarizing: v4.5.0: residualFWHM = 15.27; 1st PCA 30% v5.0.0: residualFWHM = 34.00; 1st PCA 37% (number of subjects is 53). So, it is a puzzle why the residual FWHM is that large for v5.0.0. Ed On 1 Oct 2012, at 9:15, Ed Gronenschild wrote: On 28 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 27 Date: Fri, 28 Sep 2012 10:03:47 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu Message-ID: <5065ae43.7060...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hmmm, that's a lot, but I'm very surprised that the final FWHM is over 30. How many subjects do you have? There might be one that is messed up. You can check this by loading the y.mgh as a "time course" in tksurfer. It will give you a graph with each subject. Finally, you can run mri_glmfit with the --pca option to get a PCA of the residuals. This will create a folder called pca-eres. Look at the stats.dat and see how much variance is explained by the first component (first row, 4th column). doug On 09/28/2012 03:31 AM, Ed Gronenschild wrote: Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resulting from using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Message: 16 Date: Thu, 27 Sep 2012 11:29:06 -0400 From: Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <506470c2.5060...@nmr.mgh.harvard.edu <mailto:506470c2.5060...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking that no one would ever go above it, or maybe should never go above it. I can create tables at higher smoothing levels, but 34mm is a lot of smoothing. How much did you apply to the data? doug On 09/27/2012 05:48 AM, Ed Gronenschild wrote: Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/ th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed ___ 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] No result differences v5.1.0 between MacOSX 10.6 and 10.7
Hi, For your information: for version 5.1.0 we have found no differences in the results between MacOSX 10.6 and 10.7 (53 subjects). Cheers, Ed ___ 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] Hurricane Sandy
Hi Bruce and colleagues, I hope you did survive Sandy without too much damage. Cheers, Ed ___ 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] Reference for clusterwise correction for multiple comparisons
Hi, Can you give me a reference to the method used for the clusterwise correction for multiple comparisons (CSD)? Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103? Cheers, Ed ___ 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] Problem with glmfit: matrix is ill-conditioned
Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate(s) out? Cheers, Ed > Message: 1 > Date: Thu, 24 Jan 2013 12:51:23 -0500 > From: Douglas N Greve > Subject: Re: [Freesurfer] Problem with glmfit: matrix is > ill-conditioned > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <5101749b.4060...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, the problem is that your covariates are highly correlated. Eg, > column 1 is nearly identical to column 17. > doug > > > On 01/24/2013 06:36 AM, Ed Gronenschild wrote: >> Hi, >> >> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following >> error message: >> >> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of >> continuous variables within a class. >> If you seek help with this problem, make sure to send: >> 1. Your command line: >> mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd >> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/fsgd_sib_con_cann_aangepast3.fsgd >> dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf >> fsaverage lh --C >> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/group_thickness_gender_scan_age_educ_hand_cann.mtx >> >> 2. The FSGD file (if using one) >> 3. And the design matrix above >> >> Please find attached the requested files. >> >> I noticed that rows 68 and 147 of the matrix Xg.dat are identical, >> and most probably caused the error. >> In the fsgd file I see that the correspondig cases indeed have >> identical values, although they are referring to different data. >> How to proceed? >> >> Cheers, >> Ed > ___ 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] beta
Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: > Message: 7 > Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) > From: Bruce Fischl > Subject: Re: [Freesurfer] beta > To: Colin Reveley > Cc: Joshua Lee , freesurfer@nmr.mgh.harvard.edu, >Nick Schmansky > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Colin > > yes, but we simply don't have the person power to do it at the moment. Our > FS support grant ends in a month and is not going to get renewed, so it's > going to be hard to do anytime soon. > > sorry > Bruce ___ 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] Problem with glmfit: matrix is ill-conditioned
Hi Doug, The condition numbers were: - 1e+08 for problematic fsgd file - 371.233 for previous fsgd file I tried also v5.1, however with no succes. The matirx was still ill-conditioned with condition number 2.80809e+07. Cheers, Ed On 1 Feb 2013, at 9:53, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 12 Date: Thu, 31 Jan 2013 14:08:11 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu Message-ID: <510ac11b.4090...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, that sounds strange. What were the condition numbers for the two analyses? This should be printed out into the terminal. It is also possible that it is a scaling issue. This should not be an issue in 5.1, but it is possible that it could have an effect if two columns are very similar. doug On 01/30/2013 05:10 AM, Ed Gronenschild wrote: Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate (s) out? Cheers, Ed Message: 1 Date: Thu, 24 Jan 2013 12:51:23 -0500 From: Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5101749b.4060...@nmr.mgh.harvard.edu <mailto:5101749b.4060...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, the problem is that your covariates are highly correlated. Eg, column 1 is nearly identical to column 17. doug On 01/24/2013 06:36 AM, Ed Gronenschild wrote: Hi, Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following error message: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ fsgd_sib_con_cann_aangepast3.fsgd dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf fsaverage lh --C ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ group_thickness_gender_scan_age_educ_hand_cann.mtx 2. The FSGD file (if using one) 3. And the design matrix above Please find attached the requested files. I noticed that rows 68 and 147 of the matrix Xg.dat are identical, and most probably caused the error. In the fsgd file I see that the correspondig cases indeed have identical values, although they are referring to different data. How to proceed? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] Problem with glmfit: matrix is ill-conditioned
Hi Doug, Can I do this by just permuting the contrast matrix and the corresponding columns in the fsgd file? Ed On 26 Feb 2013, at 17:43, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Hi Ed, I think it is just the way you have the matrix set up. You'll need to alter the matrix in some way. doug Message: 7 Date: Tue, 26 Feb 2013 10:08:07 +0100 From: Ed Gronenschild Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: "freesurfer@nmr.mgh.harvard.edu" Message-ID: <2031202f-e366-48cb-82a9-3142378ad...@maastrichtuniversity.nl> Content-Type: text/plain; charset="us-ascii" Hi Doug, The condition numbers were: - 1e+08 for problematic fsgd file - 371.233 for previous fsgd file I tried also v5.1, however with no succes. The matirx was still ill-conditioned with condition number 2.80809e+07. Cheers, Ed On 1 Feb 2013, at 9:53, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 12 Date: Thu, 31 Jan 2013 14:08:11 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu Message-ID: <510ac11b.4090...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, that sounds strange. What were the condition numbers for the two analyses? This should be printed out into the terminal. It is also possible that it is a scaling issue. This should not be an issue in 5.1, but it is possible that it could have an effect if two columns are very similar. doug On 01/30/2013 05:10 AM, Ed Gronenschild wrote: Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate (s) out? Cheers, Ed Message: 1 Date: Thu, 24 Jan 2013 12:51:23 -0500 From: Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5101749b.4060...@nmr.mgh.harvard.edu <mailto:5101749b.4060...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, the problem is that your covariates are highly correlated. Eg, column 1 is nearly identical to column 17. doug On 01/24/2013 06:36 AM, Ed Gronenschild wrote: Hi, Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following error message: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ fsgd_sib_con_cann_aangepast3.fsgd dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf fsaverage lh --C ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ group_thickness_gender_scan_age_educ_hand_cann.mtx 2. The FSGD file (if using one) 3. And the design matrix above Please find attached the requested files. I noticed that rows 68 and 147 of the matrix Xg.dat are identical, and most probably caused the error. In the fsgd file I see that the correspondig cases indeed have identical values, although they are referring to different data. How to proceed? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/ -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20130226/f8558727/attachment-0001.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] New Freesurfer v5.2
Hi Nick, Congratulations and thank you and the whole team (the Freesurfites) very much for your efforts. Cheers, Ed On 03 Mar, 2013, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > > Freesurfers, > > At long last, a new version of Freesurfer is available for download! > > For a list of what it contains, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > > To download it, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Download > > And remember our home page is here: > > http://surfer.nmr.mgh.harvard.edu > > Our advice concerning your data and different freesurfer versions > is the > same: do not mix versions when processing a set of subjects in your > project. > > The v5.2 default stream (recon-all -all) does not produce > significantly > different results from the v5.1 stream, so there is no compelling > reason > to re-run the default stream on your subject data. However, v5.2 > contains quite a few new features and atlases, which you can run on > data > processed by v5.1. See ReleaseNotes page for details or email the > list: > > http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Thank you to everyone who downloaded and tested the beta release of > v5.2. > > The Freesurfites > > > > > > -- > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 109, Issue 3 > ** > > > 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] cortical thickness
Hi, How do you compute the cortical thickness for each structure as listed in the ?h.aparc.stats file? Is it equal to the thickness for each vertex averaged over all vertices within each structure? Ed ___ 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] Cortical thickness - again
Hi, How do you compute the cortical thickness for each structure as listed in the ?h.aparc.stats file? Is it equal to the thickness at each vertex averaged over all vertices within the structure? Ed ___ 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] Differences in nu.mgz between v5.0.0 and v5.1.0
Hi, I noticed a difference in the file nu.mgz between FreeSurfer version v5.0.0 and v5.1.0 (running on Mac OSX10.6). It looks as if nu.mgz in v5.1.0 is an intensity scaled-down version of nu.mgz in v5.0.0. The release notes tell that a bug is fixed in mri_nu_correct.mni, I don't know if that may cause this difference. Cheers, Ed ___ 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] ICV differences from version 5.0 to 5.1
Jon, The reason is that already in one step earlier in the pipeline, the nu-correct stage, a difference arises. See thread on "Differences in nu.mgz between v5.0.0 and v5.1.0" Cheers, Ed Hi, We have noticed differences in Talairach registration (and therefore ICV estimates) in some of our subjects from version 5.0 to version 5.1. Please see the attached document. There are 4 subjects, each row represents the same subject, same input images, same recon-all options (-all) between versions. The bottom of the second page has a table with the ICV values for these subjects across versions. Have there been any changes to the Talairach registration step from 5.0 to 5.1 that would account for these differences? Thanks, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tool for filling
Hi, I'm looking for a tool to fill holes of only 1 voxel in size in a binary mask. I posted this also to the FSL mailing list but none of the suggested solutions could do this or were robust enough. Ed ___ 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] Tool for filling
Hi Bruce , What do you mean with "dev version"? Ed On 30 Sep 2011, at 15:22, Bruce Fischl wrote: > Hi Ed, > > the dev version of mri_morphology will do this: > > mri_morphology fill_holes 26 > > where the 26 specifies the min # of nbrs that must be on for the > output > voxel to be set to 1 > > cheers > Bruce > > > On Fri, 30 Sep 2011, > Ed > Gronenschild wrote: > >> Hi, >> >> I'm looking for a tool to fill holes of only 1 voxel in size >> in a binary mask. >> I posted this also to the FSL mailing list but none of the >> suggested solutions could do this or were robust enough. >> >> Ed >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for filling
Hi Bruce, I've grabbed the dev version freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ and tried mri_morphology fill_holes 26 but got the message that the operation "fill_holes" is not supported. Ed ___ 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] Tool for filling
Thank you Nick, this one works fine. Ed On 3 Oct 2011, at 17:53, Nick Schmansky wrote: > i've posted mri_morphology for the mac here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos- > leopard-intel > > n. > > > On Mon, 2011-10-03 at 11:01 -0400, Bruce Fischl wrote: >> the dev build probably didn't complete. Nick? >> On Mon, 3 Oct 2011, Ed >> Gronenschild wrote: >> >>> Hi Bruce, >>> >>> I've grabbed the dev version >>> >>> freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10) >>> at >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ >>> >>> and tried >>> >>> mri_morphology fill_holes 26 >>> >>> but got the message that the operation "fill_holes" >>> is not supported. >>> >>> Ed >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] coregistration - FA to Freesurfer
Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/ flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ 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] Diffusion tensor estimation method
Hi, There are various methods to estimate the diffusion tensor, like linear-least squares, non-linear least-squares, German-McClure M-estimator. I would like to know which method is used by FreeSurfer in the dt_recon command? Cheers, Ed ___ 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] End-of-line detection in text file
Hi, After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon? I'm on a Mac, OSX 10.6.8. Cheers, Ed ___ 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] End-of-line detection in text file
Hi Rudolph, I used TextEdit. On a Mac with OS version earlier than OS10.6 this problem didn't occur. With TextEdit it is not possible to save as UNIX format. Thanks for the trick to use sed. Ed On 9 Nov 2011, at 15:27, Rudolph Pienaar wrote: > On 11/9/11 07:59 , Ed Gronenschild wrote: >> >> After editing a text file holding the b vecs to be supplied >> as input to dt_recon this tool did not interpret the text >> file correctly. It turned out that dt_recon did not recognise >> the end-of line character in this file: this was decimal >> code 13 (called "CR"). It seems that dt_recon only >> accepts decimal code 10 (called "LF"). >> Is it possible to change dt_recon? >> >> > What did you use to edit the b-vec file? Different operating systems use > different end-of-line (EOL) conventions on text files: > > Windows: > "Old"-style (and largely depreciated) Mac: > Unix (including Mac and Linux): > > My guess is that you might have used a (possibly old) Mac-based editor to > edit your file. Often such editors have the option to save as "UNIX" format. > Choose that. > > It's not necessary to change 'dt_recon'. Simply convert your old-style Mac > text file to a new style file with: > >sed s/x0d/x0a/ old-b-vec-file > new-b-vec-file > This replaces the '0x0d' (10 in hex) characters in the file with '0x0a' (13 > in hex). > > For more details, see: > http://www.peterbenjamin.com/seminars/crossplatform/texteol.html > > > > -- > Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street, Charlestown, MA 02129 USA > > > 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] FA question
Dear Antonella, In theory, FA can be sqrt(3/2) = 1.2247449. This occurs if eigenvalues 2 and 3 are zero. You will find these high FA values (>1) mainly outside the brain. Ed On 3 Feb 2012, at 11:31, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear all, I use dt_recon to process my DTI data and get my fa.nii for the individual subjects. I wonder if the FA values can be greater that one since for all my subjects I got the FA max? value graeter than one. Is something wrong with my data or this is acceptable? I saw in? most of the papers FA<1 so 0 Thank you. Antonella ___ 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] Robust register
Hi, I would like to use mri_robust_register to co-register b-volumes to the reference b0-volume in a DTI dataset. The documentation informs that it is not quite suitable in case of large intensity differences which apply to my case. How to proceed? Is a dev version available for this purpose? Cheers, Ed ___ 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] Failure to convert DICOM files
Hi, I got an error during the first step in recon-all (Mac OS 10.6.8, FreeSurfer v5.1.0). The eror message in the log file is: WARNING: file ./MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header. This is strange because it is no mosaic file and all the files can be converted without any problems with e.g., dcm2nii and viewed with OSIRIX. Cheers, Ed ___ 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] Failure to convert DICOM files
Hi Jamaan, Yes, I got the same error. Ed On 27 Mar 2012, at 13:36, Jamaan Alghamdi wrote: > Hi Ed, > > Have you tried using mri_convert command directly without running recon-all. > > Best wishes, > Jamaan > > Hi, > > I got an error during the first step in recon-all (Mac OS 10.6.8, > FreeSurfer v5.1.0). The eror message in the log file is: > > WARNING: file > ./MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not > contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header. > > This is strange because it is no mosaic file and all the files can be > converted > without any problems with e.g., dcm2nii and viewed with OSIRIX. > > Cheers, > Ed > > -- > Jamaan Alghamdi > 07779801950 > 0151 795 4627 > Magnetic Resonance & Image Analysis Research Centre (MARIARC) > University of Liverpool > Pembroke place > Liverpool > L69 3GE > > http://www.easyneuroimaging.com/ > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed ___ 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] Failure to convert DICOM files
Hi Doug, These are Siemens DICOMs and I really don't know what happened to these T1 files, we just got them in this format. Only one out of 32 datasets went wrong, so I consider it as an incident. The workaround with dcm2nii worked fine. Nevertheless, if you are interested I can upload the dataset. Ed On 28 Mar 2012, at 15:47, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 2 Date: Tue, 27 Mar 2012 12:14:11 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] Failure to convert DICOM files To: freesurfer@nmr.mgh.harvard.edu Message-ID: <4f71e753.3040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Is it a siemens dicom? If so, what happened to the ascii header? Did you do something to the file? What are the contents of the image? Eg, a T1? doug On 03/27/2012 05:35 AM, Ed Gronenschild wrote: Hi, I got an error during the first step in recon-all (Mac OS 10.6.8, FreeSurfer v5.1.0). The eror message in the log file is: WARNING: file ./MR. 1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header. This is strange because it is no mosaic file and all the files can be converted without any problems with e.g., dcm2nii and viewed with OSIRIX. Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by "results". By the way: I always get the 8 lines with "invalid drawable" messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: > Hi Ed, > > What version of the FreeSurfer build are you using? > > Also, could you please let me know what the result is of "ls > posterior_left_CA2*"? > > Thanks, > > Koen > > > > On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild > wrote: >> Hi, >> >> I followed the instructions to visualize the hippocampal subfield >> segmentation >> by entering the command (in the subject's mri directory) >> >> freeview nu.mgz \ >>> -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ >>> -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ >>> -p-prefix posterior_ -p-lut $FREESURFER_HOME/ >>> FreeSurferColorLUT.txt >> >> and got the following messages: >> >> 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable >> 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable >> QObject::connect: Connecting from QAbstractButton::toggled(bool) >> to COMPAT slot (QGroupBox::setShown(bool)) >> QObject::connect: Connecting from QAbstractButton::toggled(bool) >> to COMPAT slot (QGroupBox::setShown(bool)) >> CTABrgbAtIndexi: index -1 was OOB >> CTABrgbAtIndexi: index -1 was OOB >> Can not find index for color name left_CA2-3 >> CTABrgbAtIndexi: index -1 was OOB >> CTABrgbAtIndexi: index -1 was OOB >> CTABrgbAtIndexi: index -1 was OOB >> Can not find index for color name right_CA2-3 >> CTABrgbAtIndexi: index -1 was OOB >> >> Nothing was shown on top of nu.mgz. All the left and righ >> posterior files >> are present. >> >> (Mac OS X 10.6.8, FreeSurfer version 5.1.0) >> >> Cheers, >> Ed >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: > Hi Ed, > > Can you please do > > "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt" > > and let me know what the result is? > > Thanks, and sorry this seems so difficult to sort out. > > Koen > > > On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild > wrote: >> Hi Koen, >> >> As already mentioned, I'm using v5.1.0, Mac Intel >> Leopard version. >> The voxel values of posterior_left_CA2-3.mgz and >> posterior_right_CA2-3.mgz are between 0 and 255, >> if that is what you mean by "results". >> By the way: I always get the 8 lines with "invalid >> drawable" messages from freeview. >> >> Ed >> >> >> On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: >> >>> Hi Ed, >>> >>> What version of the FreeSurfer build are you using? >>> >>> Also, could you please let me know what the result is of "ls >>> posterior_left_CA2*"? >>> >>> Thanks, >>> >>> Koen >>> >>> >>> >>> On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild >>> wrote: >>>> >>>> Hi, >>>> >>>> I followed the instructions to visualize the hippocampal subfield >>>> segmentation >>>> by entering the command (in the subject's mri directory) >>>> >>>> freeview nu.mgz \ >>>>> >>>>> -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ >>>>> -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ >>>>> -p-prefix posterior_ -p-lut $FREESURFER_HOME/ >>>>> FreeSurferColorLUT.txt >>>> >>>> >>>> and got the following messages: >>>> >>>> 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable >>>> 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable >>>> QObject::connect: Connecting from QAbstractButton::toggled(bool) to >>>> COMPAT slot (QGroupBox::setShown(bool)) >>>> QObject::connect: Connecting from QAbstractButton::toggled(bool) to >>>> COMPAT slot (QGroupBox::setShown(bool)) >>>> CTABrgbAtIndexi: index -1 was OOB >>>> CTABrgbAtIndexi: index -1 was OOB >>>> Can not find index for color name left_CA2-3 >>>> CTABrgbAtIndexi: index -1 was OOB >>>> CTABrgbAtIndexi: index -1 was OOB >>>> CTABrgbAtIndexi: index -1 was OOB >>>> Can not find index for color name right_CA2-3 >>>> CTABrgbAtIndexi: index -1 was OOB >>>> >>>> Nothing was shown on top of nu.mgz. All the left and righ >>>> posterior files >>>> are present. >>>> >>>> (Mac OS X 10.6.8, FreeSurfer version 5.1.0) >>>> >>>> Cheers, >>>> Ed >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person >>>> to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error >>>> and the >>>> e-mail >>>> contains patient information, please contact the Partners >>>> Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent >>>> to you in >>>> error >>>> but does not contain patient information, please contact the >>>> sender and >>>> properly >>>> dispose of the e-mail. >>>> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011. Ed On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: > OK, I see why this is not working. We've been changing some name > conventions in our internal FreeSurfer repository after the public > release of version 5.1, and somehow you managed to get an incompletely > updated version. > > It appears from > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some > versions for the Mac were updated *after* the release date (24 May > 2011), so I'll check with the engineers what exactly happened. Do you > remember which file you downloaded? > > Thanks, > > Koen > > > > On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild > wrote: >> Hi Koen, >> >> No worries. >> The result of grep is: >> >> 500 right_CA2_3 17 85 136 0 >> 550 left_CA2_3 17 85 137 0 >> >> Ed >> >> >> On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: >> >>> Hi Ed, >>> >>> Can you please do >>> >>> "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt" >>> >>> and let me know what the result is? >>> >>> Thanks, and sorry this seems so difficult to sort out. >>> >>> Koen >>> >>> >>> On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild >>> wrote: >>>> >>>> Hi Koen, >>>> >>>> As already mentioned, I'm using v5.1.0, Mac Intel >>>> Leopard version. >>>> The voxel values of posterior_left_CA2-3.mgz and >>>> posterior_right_CA2-3.mgz are between 0 and 255, >>>> if that is what you mean by "results". >>>> By the way: I always get the 8 lines with "invalid >>>> drawable" messages from freeview. >>>> >>>> Ed >>>> >>>> >>>> On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: >>>> >>>>> Hi Ed, >>>>> >>>>> What version of the FreeSurfer build are you using? >>>>> >>>>> Also, could you please let me know what the result is of "ls >>>>> posterior_left_CA2*"? >>>>> >>>>> Thanks, >>>>> >>>>> Koen >>>>> >>>>> >>>>> >>>>> On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild >>>>> wrote: >>>>>> >>>>>> >>>>>> Hi, >>>>>> >>>>>> I followed the instructions to visualize the hippocampal subfield >>>>>> segmentation >>>>>> by entering the command (in the subject's mri directory) >>>>>> >>>>>> freeview nu.mgz \ >>>>>>> >>>>>>> >>>>>>> -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ >>>>>>> -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ >>>>>>> -p-prefix posterior_ -p-lut $FREESURFER_HOME/ >>>>>>> FreeSurferColorLUT.txt >>>>>> >>>>>> >>>>>> >>>>>> and got the following messages: >>>>>> >>>>>> 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable >>>>>> 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable >>>>>> QObject::connect: Connecting from QAbstractButton::toggled >>>>>> (bool) to >>>>>> COMPAT slot (QGroupBox::setShown(bool)) >>>>>> QObject::connect: Connecting from QAbstractButton::toggled >>>>>> (bool) to >>>>>> COMPAT slot (QGroupBox::setShown(bool)) >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> Can not find index for color name left_CA2-3 >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> Can not find index for color name right_CA2-3 >>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>> >>>>>> Nothing was shown on top of nu.mgz. All the left and righ >>>>>> posterior >>>>>> files >>>>>> are present. >>>>>> >>>>>> (Mac OS X 10.6.8, FreeSurfer version 5.1.0) >>>>>> >>>>>> Cheers, >>>>>> Ed >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person >>>>>> to whom >>>>>> it >>>>>> is >>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>> and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>> sent to you >>>>>> in >>>>>> error >>>>>> but does not contain patient information, please contact the >>>>>> sender and >>>>>> properly >>>>>> dispose of the e-mail. >>>>>> >>>> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation
Hi Koen, Thanks, this solved the problem. Ed On 4 Apr 2012, at 19:21, Koen Van Leemput wrote: > Hi Ed, > > It seems that the 5.1.0 release for the Mac was composed two days > after the one for Linux, and during exactly those two days one of us > made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt. > > To correct this issue, please make a back-up copy of your > FreeSurferColorLUT.txt file, and execute the following commands: > > cd $FREESURFER_HOME > sed -i "s/CA2_3/CA2\/3/g" FreeSurferColorLUT.txt > sed -i "s/CA4_DG/CA4\/DG/g" FreeSurferColorLUT.txt > > Thanks, > > Koen > > > > > On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild > wrote: >> I have downloaded the file >> freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, >> date 26/05/2011. >> >> Ed >> >> >> On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: >> >>> OK, I see why this is not working. We've been changing some name >>> conventions in our internal FreeSurfer repository after the public >>> release of version 5.1, and somehow you managed to get an >>> incompletely >>> updated version. >>> >>> It appears from >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some >>> versions for the Mac were updated *after* the release date (24 May >>> 2011), so I'll check with the engineers what exactly happened. Do >>> you >>> remember which file you downloaded? >>> >>> Thanks, >>> >>> Koen >>> >>> >>> >>> On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild >>> wrote: >>>> >>>> Hi Koen, >>>> >>>> No worries. >>>> The result of grep is: >>>> >>>> 500 right_CA2_3 17 85 136 0 >>>> 550 left_CA2_3 17 85 137 0 >>>> >>>> Ed >>>> >>>> >>>> On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: >>>> >>>>> Hi Ed, >>>>> >>>>> Can you please do >>>>> >>>>> "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt" >>>>> >>>>> and let me know what the result is? >>>>> >>>>> Thanks, and sorry this seems so difficult to sort out. >>>>> >>>>> Koen >>>>> >>>>> >>>>> On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild >>>>> wrote: >>>>>> >>>>>> >>>>>> Hi Koen, >>>>>> >>>>>> As already mentioned, I'm using v5.1.0, Mac Intel >>>>>> Leopard version. >>>>>> The voxel values of posterior_left_CA2-3.mgz and >>>>>> posterior_right_CA2-3.mgz are between 0 and 255, >>>>>> if that is what you mean by "results". >>>>>> By the way: I always get the 8 lines with "invalid >>>>>> drawable" messages from freeview. >>>>>> >>>>>> Ed >>>>>> >>>>>> >>>>>> On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: >>>>>> >>>>>>> Hi Ed, >>>>>>> >>>>>>> What version of the FreeSurfer build are you using? >>>>>>> >>>>>>> Also, could you please let me know what the result is of "ls >>>>>>> posterior_left_CA2*"? >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Koen >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild >>>>>>> wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I followed the instructions to visualize the hippocampal >>>>>>>> subfield >>>>>>>> segmentation >>>>>>>> by entering the command (in the subject's mri directory) >>>>>>>> >>>>>>>> freeview nu.mgz \ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -p-labels posterior_left_* posterior_Left-Hippocam
[Freesurfer] recon-all processing stages
Hi I'm not sure but does the Talairach stage precede the nu-correct stage in version v5.1.0? If so, is there an option to switch these two stages? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
Hi Nick, The option -talairach-nu is not recognized in version v5.1.0. How can I proceed now? Ed On 16 Apr 2012, at 17:32, Nick Schmansky wrote: > Ed, > > Hi, no there is not an option to switch them. The nu correct stage in > 5.1 needs the talairach to run. > > However, if your intent is to get a better talairach result by > using the > nu corrected input (as it did prior to v5.1), then you can do the > following: > > recon-all -s subjid -motioncor -talairach -nuintensitycor > > then run: > > recon-all -s subjid -all -talairach-nu -clean-tal > > on the second run, it will use the nu.mgz in the talairach stage. > > Note that in the next version, v5.2, one iteration of nu_correct > will be > run prior to the talairach stage to use as input to the talairach > stage, > in order to get the better talairach results that people were seeing > prior to v5.1. it will still run the current nu_correct stage to > create > nu.mgz (the nu used in talairach gets discarded). > > Nick > > > > On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote: >> Hi, >> >> As of version 5.1 the Talairach stage precedes the nu-correction >> stage. >> Is there an option or possibility to switch this order? >> >> Cheers, >> Ed >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
Hi Nick, It does not work properly, it only produces an error message, even with no option at all: 'nknown option: '- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...]. Ed On 17 Apr 2012, at 16:28, Nick Schmansky wrote: > a modified recon-all is attached. it will run nu_correct prior to the > talairach stage, as will be the case with v5.2. so you can just run: > > recon-all -s subjid -all -clean-tal > > n. > > > On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote: >> Hi Nick, >> >> The option -talairach-nu is not recognized in version v5.1.0. >> >> How can I proceed now? >> >> Ed >> >> On 16 Apr 2012, at 17:32, Nick Schmansky wrote: >> >>> Ed, >>> >>> Hi, no there is not an option to switch them. The nu correct >>> stage in >>> 5.1 needs the talairach to run. >>> >>> However, if your intent is to get a better talairach result by >>> using the >>> nu corrected input (as it did prior to v5.1), then you can do the >>> following: >>> >>> recon-all -s subjid -motioncor -talairach -nuintensitycor >>> >>> then run: >>> >>> recon-all -s subjid -all -talairach-nu -clean-tal >>> >>> on the second run, it will use the nu.mgz in the talairach stage. >>> >>> Note that in the next version, v5.2, one iteration of nu_correct >>> will be >>> run prior to the talairach stage to use as input to the talairach >>> stage, >>> in order to get the better talairach results that people were seeing >>> prior to v5.1. it will still run the current nu_correct stage to >>> create >>> nu.mgz (the nu used in talairach gets discarded). >>> >>> Nick >>> >>> >>> >>> On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote: >>>> Hi, >>>> >>>> As of version 5.1 the Talairach stage precedes the nu-correction >>>> stage. >>>> Is there an option or possibility to switch this order? >>>> >>>> Cheers, >>>> Ed >>>> ___ >>>> 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] Error with recon-all
Hi, I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject. recon-all stopped and issued the following error: cp: ../surf/lh.orig_corrected: No such file or directory. Note that I included the option -no-wsgcaatlas to get a better skullstripping because in the default mode the skulltripping was bad. With this option it looks good. I got the above error regularly for other subjects as well and by including the -no-wsgcaatlas option recon-all finished without error, except for the present case. Cheers, Ed ___ 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] Error with recon-all
Hi Nick, Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore. Cheers, Ed On 9 May 2012, at 18:53, Nick Schmansky wrote: > can you send the recon-all.log file? does it say why the > lh.orig_corrected file wasnt created? > > On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote: >> Hi, >> >> I'm using the version of recon-all that Nick provided >> at April 17 to be able to run nu_correct prior to the >> Talairach stage. (I'm on a Mac, OSX 10.6, version >> v5.1.0). The command given was >> >> recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ >> -clean-tal -s subject. >> >> recon-all stopped and issued the following error: >> >> cp: ../surf/lh.orig_corrected: No such file or directory. >> >> Note that I included the option -no-wsgcaatlas to get >> a better skullstripping because in the default mode >> the skulltripping was bad. With this option it looks >> good. >> I got the above error regularly for other subjects as well >> and by including the -no-wsgcaatlas option recon-all >> finished without error, except for the present case. >> >> Cheers, >> Ed >> ___ >> 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] recon-all settings
Hi, I want to use parameters different from default for mri_nu_correct.mni. This command uses nu_correct for which I would like to set the following options: -distance 25 -stop 0.0001 -fwhm 0.1 These settings are more approriate when using 3T T1 data. How can I invoke these in recon-all? Can I use an options file? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Option --fwhm with command mri_nu_correct.mni
Hi I tried to use option --fwhm 0.1 with mri_nu_correct.mni and noticed that this is incorrectly interpreted as option --distance 0.1. This script reads if($#FWHM) set cmd = ($cmd -distance $FWHM); whereas this should be if($#FWHM) set cmd = ($cmd -fwhm $FWHM); Is it possible to correct the mri_nu_correct.mni script? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with space in directory or file name
Hi, Whenever I want to convert DICOM files to .mgz file I have to remove spaces in the directory name or file names otherwise recon-all -i ... -s ... will not work. Bracketing the names within quotes will not help. Is there some workaround? ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with space in directory or file name
Hi Sita, That doesn't work. I have to write a script to remove the space. ed On 7 May 2009, at 1:15, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Hi Ed, You can try inserting a backslash and then a space in the filename. eg.. if you have 'dicom file.dcm', you might want to try recon-all -all -i dicom\ file.dcm -s . Sita. On Wed, 6 May 2009, Ed Gronenschild wrote: Hi, Whenever I want to convert DICOM files to .mgz file I have to remove spaces in the directory name or file names otherwise recon-all -i ... -s ... will not work. Bracketing the names within quotes will not help. Is there some workaround? ed ___ 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
[Freesurfer] Error with skullstripping
Hi, During processing with the command recon-all autorecon-all -s mysubject I got an error with the following message: mri_watershed error: GLOBAL region of the brain empty ! What to do? Can I use a different option for the watershed algoritme? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Measurement voxel space
Hi, To which voxel space (native, Talairach or any other standard space) do the measured cortical thickness and areas/volumes in the statistical output files refer? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extraction of WM + GM Volumes
Hi, I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extraction of WM + GM Volumes
Doug, The file "segmentation.mgz" doesn't exist. I think that you mean that segmentation.mgz stands for either WM or GM. Can you provide me the exact file names of the final WM and GM segmentations. Ed On 25 Aug 2009, at 17:28, Douglas N Greve wrote: > mri_convert segmentation.mgz segmentation.nii > > should do it > > doug > > Ed Gronenschild wrote: >> Hi, >> >> I would like to extract the WM and GM segmentations >> used for the final cortical thickness calculations as >> nifti files. How can I do that? >> >> Ed >> >> ___ >> 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extraction of WM + GM Volumes
Doug, I want all GM. Ed On 26 Aug, 2009, at 18:53 , freesurfer-requ...@nmr.mgh.harvard.edu wrote: For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want a particular GM or all GM? Ed Gronenschild wrote: Doug, The file "segmentation.mgz" doesn't exist. I think that you mean that segmentation.mgz stands for either WM or GM. Can you provide me the exact file names of the final WM and GM segmentations. Ed On 25 Aug 2009, at 17:28, Douglas N Greve wrote: mri_convert segmentation.mgz segmentation.nii should do it doug Ed Gronenschild wrote: Hi, I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that? Ed ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with topology fixing
Hi, I got the following error during processing my subject nr 104 with recon-all: ERROR: - FindPacePath: could not find path. The error log tells that it occurred during execution of the command mris_topo_fixer -mgz -warnings 104 rh What to do? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with topology fixing
Hi Bruce, The log file tells that mris_fix_topology did fail (euler number != 2) and that's why the topo_fixer was used. Ed On 1 Sep 2009, at 15:12, Bruce Fischl wrote: > did you try using the old (default) topology fixer? Usually > mris_fix_topology is called in recon-all unless you specify otherwise. > > cheers, > Bruce > On > Tue, 1 Sep 2009, Ed Gronenschild wrote: > >> Hi, >> >> I got the following error during processing my subject nr 104 with >> recon-all: >> >> ERROR: - FindPacePath: could not find path. >> >> The error log tells that it occurred during execution of the command >> >> mris_topo_fixer -mgz -warnings 104 rh >> >> What to do? >> >> Ed >> >> ___ >> 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
Re: [Freesurfer] Problem with topology fixing
Bruce, You're right: the skullstripping didn't go well so that part of the skull is still present. I'll try to fix that. Thanks, Ed On 1 Sep 2009, at 16:03, Bruce Fischl wrote: > I see. Have you looked at the orig.nofix surface? If there is a huge > defect (e.g. cerebellum or skull connected to cortex) then things > will fail. Make sure nothing is dramatically wrong with it or the > aseg.mgz > first. > > Bruce > > > On > Tue, 1 Sep 2009, Ed Gronenschild wrote: > >> Hi Bruce, >> >> The log file tells that mris_fix_topology did fail (euler number ! >> = 2) >> and that's why the topo_fixer was used. >> >> Ed >> >> On 1 Sep 2009, at 15:12, Bruce Fischl wrote: >> >>> did you try using the old (default) topology fixer? Usually >>> mris_fix_topology is called in recon-all unless you specify >>> otherwise. >>> >>> cheers, >>> Bruce >>> On >>> Tue, 1 Sep 2009, Ed Gronenschild wrote: >>> >>>> Hi, >>>> >>>> I got the following error during processing my subject nr 104 with >>>> recon-all: >>>> >>>> ERROR: - FindPacePath: could not find path. >>>> >>>> The error log tells that it occurred during execution of the >>>> command >>>> >>>> mris_topo_fixer -mgz -warnings 104 rh >>>> >>>> What to do? >>>> >>>> Ed >>>> >>>> ___ >>>> 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 >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] poll question: Mac OS Tiger users
Hi Nick, I'm using Freesurfer on different Macs, of which one with Tiger OS and ppc. So, I kindly ask you to continue support for Tiger OS and ppc for at least this year. Ed On 13 Jan 2010, at 23:14, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > > for the Mac OS users out there: > > who still needs a Tiger OS build of freesurfer? and on what processor > (intel or ppc)? > > i'd like to discontinue support for Tiger (and redirect efforts toward > working with Snow Leopard), but if enough people still need the Tiger > build then we can keep our creaky-old machine around to do this. > > Nick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt-recon output file format
Hi, Question for the developers. Is it possible to adjust the dt-recon tool such that the output files are in zipped NIFTI format (.nii.gz) in view of the enormous amount of data that is generated. It can accept .nii.gz files as input. Thank you in advance, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] dt-recon output file format
Bruce, Is it .niz or nii.gz? Ed On 9 Feb 2010, at 15:04, Bruce Fischl wrote: > Hi Ed, > > we should add this as the default, but for now you can just go into > the > dt_recon script and do a global replace of: > > .nii --> .niz > > cheers, > Bruce > > > On Tue, 9 Feb 2010, Ed > Gronenschild wrote: > >> Hi, >> >> Question for the developers. >> Is it possible to adjust the dt-recon tool such that >> the output files are in zipped NIFTI format (.nii.gz) >> in view of the enormous amount of data that is >> generated. It can accept .nii.gz files as input. >> >> Thank you in advance, >> Ed >> >> ___ >> 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
[Freesurfer] Bad pial surface
Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Intel. Ed ___ 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] Problem with tkmedit Edit Voxels Tool on Intel Mac
Hi, On an Intel Mac the Edit Voxels Tool does not work, contrary to a PPC Mac. This applies both to version v4.3.1 and v4.5.0. Ed ___ 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] Problem with tkmedit Edit Voxels Tool on Intel Mac
Hi, I post this message once again because I didn't get any reply. On an Intel Mac the "Edit Voxels Tool" in tkmedit does not work, contrary to a PPC Mac. This applies both to version v4.3.1 and v4.5.0. Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to find out which package of FSL is used by FreeSurfer
Hi, The FreeSurfer package is bundled with a subset of FSL. However, I think most of us also installed the full FSL package. The global variable FSL_DIR points to the directory of FSL. My question is if it is possible to read from recon-all log files which FSL package is used? Ed ___ 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] Bad pial surface - continued
Hi,
I've mailed this once before and tried to solve a persistent problem.
Reviewing the results of recon-all I noticed that the derived pial
surface chopped away an unacceptable amount of gm voxels.
First of all I tried to manually edit some wm voxels, however with
no success.
Then I tried another solution by combining the FSL-FAST wm
segmentation with wm.mgz because I noticed that FSL_FAST
produced better results. Although the results did improve,
still the pial surface was incorrect.
The last option I tried was another set of parameters for
nu_correct. Because it concerns 3T scans I used
--proto-iters1000 and --distance 50 (see paper of Zheng et al,
NeuroImage 48, 73-83 (2009)) and previous e-mails on
this subject ("nu-correct parameters", 27 April 2010).
Also with these settings the pial surface chopped away
too many voxels.
I'm desperate, the manuals provide no options on how to fix
such problems. The pial surface can be corrected by only
REMOVING voxels that are included erroneously but there is
no way to extent the pial surface by ADDING voxels.
Ed
___
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[Freesurfer] Which volumes to use
Hi, I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files: - aseg.mgz - aseg.stats - aparc+aseg.mgz - wmparc.mgz - wmparc.stats To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects. The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring? Ed ___ 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] Which volumes to use
But what about the labels starting with "lh-ctx-" and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). In the wmparc.stats file it has a volume of 8249 voxels and in wmparc.mgz 8752 voxels? Is the first pve-corrected and the latter not? On 18 Jun, 2010, at 13:43, Allison Stevens wrote: > You're right - aseg.stats refers to the aseg.mgz and you should use > that. > You would only use the wm parcellations from the wmparc.mgz > > -- > > On Fri, 18 Jun 2010, Ed Gronenschild wrote: > >> Hi, >> >> I tried to find out this from previous contributions >> but got lost. >> There's some confusion on which file(s) to use >> for segmented volumes. >> FreeSurfer generates the following image and >> text files: >> - aseg.mgz >> - aseg.stats >> - aparc+aseg.mgz >> - wmparc.mgz >> - wmparc.stats >> >> To my best knowledge aseg.stats contains >> the volumes from the structures in aseg.mgz, >> but corrected for partial volume effects. >> >> The volumes listed in the aseg.stats and >> wmparc.stats are in most cases different. >> Which volumes are the correct ones and >> to which of the image files are these >> referring? >> >> Ed >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Which volumes to use
Doug, I don't understand this since the ?h.aparc.stats file doesn't contain volumes. Ed On 18 Jun, 2010, at 15:56, Douglas N Greve wrote: > Yes, the difference is partial volume correction. But you should > use the > values from the ?h.aparc.stats file for cortical parcellations as it > uses the more accurate surface-based volumetric calculation. > > doug > > Ed Gronenschild wrote: >> But what about the labels starting with "lh-ctx-" >> and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). >> In the wmparc.stats file it has a volume of 8249 >> voxels and in wmparc.mgz 8752 voxels? >> Is the first pve-corrected and the latter not? >> >> On 18 Jun, 2010, at 13:43, Allison Stevens wrote: >> >> >>> You're right - aseg.stats refers to the aseg.mgz and you should use >>> that. >>> You would only use the wm parcellations from the wmparc.mgz >>> >>> -- >>> >>> On Fri, 18 Jun 2010, Ed Gronenschild wrote: >>> >>> >>>> Hi, >>>> >>>> I tried to find out this from previous contributions >>>> but got lost. >>>> There's some confusion on which file(s) to use >>>> for segmented volumes. >>>> FreeSurfer generates the following image and >>>> text files: >>>> - aseg.mgz >>>> - aseg.stats >>>> - aparc+aseg.mgz >>>> - wmparc.mgz >>>> - wmparc.stats >>>> >>>> To my best knowledge aseg.stats contains >>>> the volumes from the structures in aseg.mgz, >>>> but corrected for partial volume effects. >>>> >>>> The volumes listed in the aseg.stats and >>>> wmparc.stats are in most cases different. >>>> Which volumes are the correct ones and >>>> to which of the image files are these >>>> referring? >>>> >>>> Ed >>>> >>>> ___ >>>> 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 >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Which volumes
Hi, In the wmparc.stats file a large number of ctx structures and the corresponding volumes, like ctx-lh-parahippocampal. For some of these structures the volumes are also listed in the ?h.aparc.stats files. Which volumes are correct? Ed ___ 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] CSF volume
Hi, One of the volumes listed in the aseg.stats is called "CSF". Its volume is too small to indicate the total CSF volume of the brain. What is its meaning? If I would like to get the total CSF volume how should I proceed? Ed ___ 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] Meaning of volumes
Hi, What exactly is the definition of - Brain Mask Volume - Brain Segmentation Volume as listed in the aseg.stats file? Moreover, and correct me if I'm wrong, the Intracranial volume is the scaled intracranial volume of the MNI template. Is the latter intracranial volume just a number or is it available in 3D as an image file? I would like to know how it is defined. Kind regards, Ed ___ 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] Error with mri_segstats
Hi, I'm trying to use mri_segstats and get the following error: ERROR: could not open stats/aseg1.stats for writing The full command I gave was: mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / Applications/freesurfer/ASegStatsLUT.txt --subject C001 The SUBJECTS_DIR was set to the directory containing the subject C001. I have full privileges to read/write to all folders. If I try to write to just aseg1.stats (so using option --sum aseg1.stats) I get the error message that aseg.mgz could not be opened. I'm on a Mac using FreeSurfer v5.0.0. Ed ___ 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] Total GM and WM volumes
Hi, In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed ___ 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] Total GM and WM volumes - again
Hi, I post this once again because I didn't get any response. In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed ___ 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] Total GM and WM volumes
Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 - 251139 = 281628 gm rh = 536127 - 254730 = 281397 Left + right: total = 1068894 wm = 505869 gm = 563025 The aseg.stats file lists the following results: cortical wm lh: 251139 cortical wm rh: 254730 total wm: 505869 cortical gm lh: 263888 cortical gm rh: 265231 total cortical gm: 529119 subcortical gm: 181270 total gm: 710389 -- For wm both results are equal but for gm they are not. So now my question still exists: which wm and gm volumes should I take? Ed On 26 Oct 2010, at 20:40, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Ed, to my knowledge, "mris_wm_volume" is the best option to determine the white matter volume. See this wiki page for usage: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Best wishes, Christian --- Christian Scheel Department of Psychiatry University of Cologne Am 26.10.2010 15:22, schrieb Ed Gronenschild: Hi, I post this once again because I didn't get any response. In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed ___ 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] Total GM and WM volumes
Dear Bruce/Allison, Could you please try to give response to my question which wm and gm volumes I shoud use, see my today's submission below. Ed On 27 Oct 2010, at 14:41, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 - 251139 = 281628 gm rh = 536127 - 254730 = 281397 Left + right: total = 1068894 wm = 505869 gm = 563025 The aseg.stats file lists the following results: cortical wm lh: 251139 cortical wm rh: 254730 total wm: 505869 cortical gm lh: 263888 cortical gm rh: 265231 total cortical gm: 529119 subcortical gm: 181270 total gm: 710389 -- For wm both results are equal but for gm they are not. So now my question still exists: which wm and gm volumes should I take? Ed On 26 Oct 2010, at 20:40, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Ed, to my knowledge, "mris_wm_volume" is the best option to determine the white matter volume. See this wiki page for usage: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Best wishes, Christian --- Christian Scheel Department of Psychiatry University of Cologne Am 26.10.2010 15:22, schrieb Ed Gronenschild: Hi, I post this once again because I didn't get any response. In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed ___ 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] Total GM and WM volumes
Hi Allison, Thanks. It is still confusing: for the gm the aseg.stats lists cortical as well as subcortical and the total volumes (being the sum of both). But for wm only cortical volumes are present. Is there no subcortical wm volume present or defined? Ed On 27 Oct 2010, at 15:58, Allison Stevens wrote: Ed, I would use the values in the aseg.stats. I'm not sure why there is this difference (Doug might be able to elaborate on how the values in aseg.stats are calculated) but for v5.0, we went over how all the stats were being calculated and make sure the values in the aseg.stats were the most accurate. Allison -- On Wed, 27 Oct 2010, Ed Gronenschild wrote: Dear Bruce/Allison, Could you please try to give response to my question which wm and gm volumes I shoud use, see my today's submission below. Ed On 27 Oct 2010, at 14:41, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 - 251139 = 281628 gm rh = 536127 - 254730 = 281397 Left + right: total = 1068894 wm = 505869 gm = 563025 The aseg.stats file lists the following results: cortical wm lh: 251139 cortical wm rh: 254730 total wm: 505869 cortical gm lh: 263888 cortical gm rh: 265231 total cortical gm: 529119 subcortical gm: 181270 total gm: 710389 -- For wm both results are equal but for gm they are not. So now my question still exists: which wm and gm volumes should I take? Ed On 26 Oct 2010, at 20:40, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Ed, to my knowledge, "mris_wm_volume" is the best option to determine the white matter volume. See this wiki page for usage: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Best wishes, Christian --- Christian Scheel Department of Psychiatry University of Cologne Am 26.10.2010 15:22, schrieb Ed Gronenschild: Hi, I post this once again because I didn't get any response. In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed 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] 3 button mouse for macintosh
Dear Isabelle, In the System Preferences -> Keyboard & Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed Hello, Just getting started with Freesurfer. I'm hoping someone can recommend a 3-button mouse that works well with Freesurfer, on a Macintosh. I purchased a Logitech wireless mouse, but can't get it to work properly. Freesurfer does not seem to recognize the 2nd and 3rd buttons as any different than the 1st/ left button. So I cannot get edits to work, for example, when trying to edit white matter. Any tips appreciated. -Isabelle - Isabelle M. Rosso, Ph.D. Assistant Professor of Psychology Licensed Psychologist -- Certified Health Service Provider McLean Hospital Neuroimaging Center 115 Mill Street Belmont, MA 02478 Phone: 617.855.2607 Fax: 617.855.2770 iro...@hms.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Output dt_recon
Hi, Is it possible to give the exact definition of the output of dt_recon, in particular: - adc - ra - radialdiff - ivc Ed ___ 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] Total GM and WM volumes
Hi Doug, I checked the numbers again and found the difference: The last occurrence in the recon-all.log reads: Getting Cerebral WM volumes from surface lh white matter volume 251139 rh white matter volume 254730 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 268878.928656, pTot = 532766.945301 c = 263888.016645 rh surface-based volumes (mm3): wTot = 270895.731618, pTot = 536126.997702 c = 265231.266084 Output from mris_volume: lh.pial = 532766.945301 rh.pial = 536126.997702 lh.white = 268878.928656 rh.white = 270895.731618 These numbers are exactly equal to those in recon-all.log (pTot and wTot, respectively). So far so good. Now I turn to the output in aseg.stats which read: # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 263888.016645, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 265231.266084, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 529119.282729, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 251139.437500, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 254729.859375, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 505869.296875, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 181270.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 710389.282729, mm^3 Now I get confused: The gray matter volumes "?hCortexVol" are equal to the volumes "c" in recon-all.log. But the white matter volumes "?hCorticalWhiteMatter" differ from "wTot" in recon-all.log. However, they are equal to the volumes listed below the line "Getting Cerebral WM volumes from surface" in recon-all.log. (these volumes are also equal to those computed with mris_wm_volume). What's the difference betwen these white matter volumes? In summary: the gray matter volumes in recon-all.log and aseg.stats are equal, but the white matter volumes differ. Which white matter volumes should I use? Ed On 29 Oct 2010, at 22:36, Douglas N Greve wrote: > > Hi Ed, I can't replicate this. Can you double check your numbers > again? > In particular, can you compare them against numbers that are > printed in > the recon-all.log file? > > In recon-all.log, look for the lines >Getting Cerebral GM and WM volumes from surfaces >lh surface-based volumes (mm3): wTot = 244767.110356, pTot = > 436943.557923 c = 192176.447567 >rh surface-based volumes (mm3): wTot = 243959.351030, pTot = > 438113.303648 c = 194153.952618 > > These might be repeated through out the file if you're re-run. Make > sure > they are the last set. > > The wTot and pTot should give you the same values as mris_volume > ?h.white and mris_volume ?h.pial > It does when I run it here. > > doug > > > Ed Gronenschild wrote: >> Dear Christian, >> >> Thanks for your suggestion. I followed the instructions to derive the >> GM and WM volumes. Here are the (rounded-off) results for one >> example: >> >> mris_volume lh.pial: 532767 >> mris_volume rh.pial: 536127 >> >> mris_wm_volume lh: 251139 >> mris_wm_volume rh: 254730 >> >> Accordingly: >> gm lh = 532767 - 251139 = 281628 >> gm rh = 536127 - 254730 = 281397 >> >> Left + right: >> total = 1068894 >> wm = 505869 >> gm = 563025 >> >> >> >> The aseg.stats file lists the following results: >> >> cortical wm lh: 251139 >> cortical wm rh: 254730 >> total wm: 505869 >> >> cortical gm lh: 263888 >> cortical gm rh: 265231 >> total cortical gm: 529119 >> subcortical gm: 181270 >> total gm: 710389 >> >> -- >> >> For wm both results are equal but for gm they are not. >> >> So now my question still exists: which wm and gm volumes should I >> take? >> >> Ed >> >> >> On 26 Oct 2010, at 20:40, freesurfer-requ...@nmr.mgh.harvard.edu >> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >> >>> Dear Ed, >>> >>> to my knowledge, "mris_wm_volume" is the best option to determine >>> the >>> white matter volume. >>> >>> See this wiki page for usage: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >>> >>> Best wishes, >>> Christian >>> >>> >>> --- >>> Christian Scheel >>&
Re: [Freesurfer] Total GM and WM volumes
Hi Doug, This thread about GM and WM volumes was initiated by my question on how to get the total cerebral GM and WM volumes. From what I understand now is that for the GM I should take the volume named "TotalGray" in the aseg.stats file. In the example below that would be 710389.282729. However, for the total cerebral WM volume I can't use the aseg.stats file because the measure "CorticalWhiteMatter" is ony the cortical white matter volume and does not include the subcortical white matter. Instead I should compute it by means of mris_volume lh.white + rh.white. Is that right? The alternative would be to derive the subcortical white matter volume from one of the stats files and add it to the cortical white matter. Is that possible and if so, how? Ed On 3 Nov 2010, at 15:58, Douglas N Greve wrote: > Ah, the "white matter" volume computed from the pial-white includes > the > subcortical structures. Once those are subtracted, you should get > the #s > in the aseg.stats file. > > doug > > Ed Gronenschild wrote: >> Hi Doug, >> >> I checked the numbers again and found the difference: >> >> The last occurrence in the recon-all.log reads: >> >> Getting Cerebral WM volumes from surface >> lh white matter volume 251139 >> rh white matter volume 254730 >> Getting Cerebral GM and WM volumes from surfaces >> lh surface-based volumes (mm3): wTot = 268878.928656, pTot = >> 532766.945301 c = 263888.016645 >> rh surface-based volumes (mm3): wTot = 270895.731618, pTot = >> 536126.997702 c = 265231.266084 >> >> Output from mris_volume: >> lh.pial = 532766.945301 >> rh.pial = 536126.997702 >> lh.white = 268878.928656 >> rh.white = 270895.731618 >> These numbers are exactly equal to those in recon-all.log (pTot and >> wTot, respectively). >> So far so good. >> >> Now I turn to the output in aseg.stats which read: >> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter >> volume, 263888.016645, mm^3 >> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray >> matter volume, 265231.266084, mm^3 >> # Measure Cortex, CortexVol, Total cortical gray matter volume, >> 529119.282729, mm^3 >> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left >> hemisphere cortical white matter volume, 251139.437500, mm^3 >> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right >> hemisphere cortical white matter volume, 254729.859375, mm^3 >> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical >> white matter volume, 505869.296875, mm^3 >> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter >> volume, 181270.00, mm^3 >> # Measure TotalGray, TotalGrayVol, Total gray matter volume, >> 710389.282729, mm^3 >> >> Now I get confused: >> The gray matter volumes "?hCortexVol" are equal to the volumes "c" in >> recon-all.log. >> But the white matter volumes "?hCorticalWhiteMatter" differ from >> "wTot" in recon-all.log. >> However, they are equal to the volumes listed below the line "Getting >> Cerebral WM volumes from surface" >> in recon-all.log. (these volumes are also equal to those computed >> with mris_wm_volume). >> What's the difference betwen these white matter volumes? >> >> In summary: the gray matter volumes in recon-all.log and aseg.stats >> are equal, >> but the white matter volumes differ. >> Which white matter volumes should I use? >> >> Ed >> >> >> On 29 Oct 2010, at 22:36, Douglas N Greve wrote: >> >> >>> Hi Ed, I can't replicate this. Can you double check your numbers >>> again? >>> In particular, can you compare them against numbers that are >>> printed in >>> the recon-all.log file? >>> >>> In recon-all.log, look for the lines >>> Getting Cerebral GM and WM volumes from surfaces >>> lh surface-based volumes (mm3): wTot = 244767.110356, pTot = >>> 436943.557923 c = 192176.447567 >>> rh surface-based volumes (mm3): wTot = 243959.351030, pTot = >>> 438113.303648 c = 194153.952618 >>> >>> These might be repeated through out the file if you're re-run. Make >>> sure >>> they are the last set. >>> >>> The wTot and pTot should give you the same values as mris_volume >>> ?h.white and mris_volume ?h.pial >>> It does when I run it here. >>> >>> doug >>> >>> >>> Ed Gronenschild wrote: >>> >>>>
Re: [Freesurfer] Total GM and WM volumes
Hi Michael, Thanks for your explanation. It was rather confusing but the picture is now clear: for the total cerebral white matter I should take the measure "CorticalWhiteMatter" in the aseg.stats. Ed On 4 Nov 2010, at 15:05, Michael Harms wrote: > > Hi Ed, > Is there a distinction in FreeSurfer between "cortical" and > "subcortical" white matter? I thought that white matter was simply > white matter... > > You wrote that the white matter values in aseg.stats are identical to > the output of mris_wm_volume, which is exactly what I would expect. > > You do NOT want to use the output of mris_volume on lh.white and > rh.white as a measure of white matter volume, as that will include > subcortical gray as well as the ventricles. (mris_volume simply > returns > the total volume enclosed within the input surface, and since the > lh/rh.white surfaces also "enclose" the subcortical gray and > ventricles, > those would be included in the total. The whole purpose of > mris_wm_volume is to remove those structures from the WM volume > calculation). > > cheers, > -MH > > > On Thu, 2010-11-04 at 10:15 +0100, Ed Gronenschild wrote: >> Hi Doug, >> >> This thread about GM and WM volumes was initiated by my question >> on how to get the total cerebral GM and WM volumes. >> >> From what I understand now is that for the GM I should take the >> volume named "TotalGray" in the aseg.stats file. In the example >> below that would be 710389.282729. >> >> However, for the total cerebral WM volume I can't use the aseg.stats >> file because the measure "CorticalWhiteMatter" is ony the cortical >> white matter volume and does not include the subcortical >> white matter. Instead I should compute it by means of >> mris_volume lh.white + rh.white. Is that right? >> The alternative would be to derive the subcortical white matter >> volume from one of the stats files and add it to the cortical >> white matter. Is that possible and if so, how? >> >> Ed >> >> >> On 3 Nov 2010, at 15:58, Douglas N Greve wrote: >> >>> Ah, the "white matter" volume computed from the pial-white includes >>> the >>> subcortical structures. Once those are subtracted, you should get >>> the #s >>> in the aseg.stats file. >>> >>> doug >>> >>> Ed Gronenschild wrote: >>>> Hi Doug, >>>> >>>> I checked the numbers again and found the difference: >>>> >>>> The last occurrence in the recon-all.log reads: >>>> >>>> Getting Cerebral WM volumes from surface >>>> lh white matter volume 251139 >>>> rh white matter volume 254730 >>>> Getting Cerebral GM and WM volumes from surfaces >>>> lh surface-based volumes (mm3): wTot = 268878.928656, pTot = >>>> 532766.945301 c = 263888.016645 >>>> rh surface-based volumes (mm3): wTot = 270895.731618, pTot = >>>> 536126.997702 c = 265231.266084 >>>> >>>> Output from mris_volume: >>>> lh.pial = 532766.945301 >>>> rh.pial = 536126.997702 >>>> lh.white = 268878.928656 >>>> rh.white = 270895.731618 >>>> These numbers are exactly equal to those in recon-all.log (pTot and >>>> wTot, respectively). >>>> So far so good. >>>> >>>> Now I turn to the output in aseg.stats which read: >>>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray >>>> matter >>>> volume, 263888.016645, mm^3 >>>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray >>>> matter volume, 265231.266084, mm^3 >>>> # Measure Cortex, CortexVol, Total cortical gray matter volume, >>>> 529119.282729, mm^3 >>>> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left >>>> hemisphere cortical white matter volume, 251139.437500, mm^3 >>>> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right >>>> hemisphere cortical white matter volume, 254729.859375, mm^3 >>>> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total >>>> cortical >>>> white matter volume, 505869.296875, mm^3 >>>> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter >>>> volume, 181270.00, mm^3 >>>> # Measure TotalGray, TotalGrayVol, Total gray matter volume, >>>> 710389.282729, mm^3 >>>> >>>> Now I get confused: >>>> The gray matter volume
Re: [Freesurfer] Total GM and WM volumes
Hi Doug, I'm sorry about using the term "subcortical white matter". It was due to misunderstanding your response, viz. "the white matter volume computed from the pial-white includes subcortical structures". It's settled now, see response by Michael Harms and my reponse to that. Ed On 4 Nov 2010, at 16:23, Douglas N Greve wrote: > Hi Ed, > > What do you mean by subcortical white matter? Do you mean cerebellar > white matter? The mris_volume command will give you the entire volume > inside the white surface, which will include all gray matter > structures. > This will not include cerebellar white matter. > > doug > > Ed Gronenschild wrote: >> Hi Doug, >> >> This thread about GM and WM volumes was initiated by my question >> on how to get the total cerebral GM and WM volumes. >> >> From what I understand now is that for the GM I should take the >> volume named "TotalGray" in the aseg.stats file. In the example >> below that would be 710389.282729. >> >> However, for the total cerebral WM volume I can't use the aseg.stats >> file because the measure "CorticalWhiteMatter" is ony the cortical >> white matter volume and does not include the subcortical >> white matter. Instead I should compute it by means of >> mris_volume lh.white + rh.white. Is that right? >> The alternative would be to derive the subcortical white matter >> volume from one of the stats files and add it to the cortical >> white matter. Is that possible and if so, how? >> >> Ed >> >> >> On 3 Nov 2010, at 15:58, Douglas N Greve wrote: >> >>> Ah, the "white matter" volume computed from the pial-white >>> includes the >>> subcortical structures. Once those are subtracted, you should get >>> the #s >>> in the aseg.stats file. >>> >>> doug >>> >>> Ed Gronenschild wrote: >>>> Hi Doug, >>>> >>>> I checked the numbers again and found the difference: >>>> >>>> The last occurrence in the recon-all.log reads: >>>> >>>> Getting Cerebral WM volumes from surface >>>> lh white matter volume 251139 >>>> rh white matter volume 254730 >>>> Getting Cerebral GM and WM volumes from surfaces >>>> lh surface-based volumes (mm3): wTot = 268878.928656, pTot = >>>> 532766.945301 c = 263888.016645 >>>> rh surface-based volumes (mm3): wTot = 270895.731618, pTot = >>>> 536126.997702 c = 265231.266084 >>>> >>>> Output from mris_volume: >>>> lh.pial = 532766.945301 >>>> rh.pial = 536126.997702 >>>> lh.white = 268878.928656 >>>> rh.white = 270895.731618 >>>> These numbers are exactly equal to those in recon-all.log (pTot and >>>> wTot, respectively). >>>> So far so good. >>>> >>>> Now I turn to the output in aseg.stats which read: >>>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray >>>> matter >>>> volume, 263888.016645, mm^3 >>>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray >>>> matter volume, 265231.266084, mm^3 >>>> # Measure Cortex, CortexVol, Total cortical gray matter volume, >>>> 529119.282729, mm^3 >>>> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left >>>> hemisphere cortical white matter volume, 251139.437500, mm^3 >>>> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right >>>> hemisphere cortical white matter volume, 254729.859375, mm^3 >>>> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total >>>> cortical >>>> white matter volume, 505869.296875, mm^3 >>>> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter >>>> volume, 181270.00, mm^3 >>>> # Measure TotalGray, TotalGrayVol, Total gray matter volume, >>>> 710389.282729, mm^3 >>>> >>>> Now I get confused: >>>> The gray matter volumes "?hCortexVol" are equal to the volumes >>>> "c" in >>>> recon-all.log. >>>> But the white matter volumes "?hCorticalWhiteMatter" differ from >>>> "wTot" in recon-all.log. >>>> However, they are equal to the volumes listed below the line >>>> "Getting >>>> Cerebral WM volumes from surface" >>>> in recon-all.log. (these volumes are also equal to those computed >>>> with mris_wm
