Re: [Freesurfer] brain mask and T1 are not the same size
To try to understand the problem as to why the brainmask.mgz and T1.mgz files are not the same size, I decided to skip that step and make edits to the white matter only. At this point, all files (i.e. T1.mgz, brainmask.mgz and the wm.mgz) have the same dimensions 256^3. I removed offending voxels from the wm.mgz file using Freeview as per the instructions found on this website: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview. For all participants except 4, the modifications did not result in in errors. However, for the same 4 participants that had problems with the brainmask.mgz file, I have problems with the wm edits after running : recon-all -autorecon2-wm -autorecon3 -subjid S08_FS This is the error that I got: ERROR: mri_segment-MRIcheckVolDims: volume1 height=255 != volume2 height=256. Darwin Isabelles-iMac.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s S08_FS exited with ERRORS at Tue Aug 9 13:44:25 EDT 2016 It appears that for these 4 participants that are problematic, any corrections made to the brainmask or wm.mgz file changes the dimensions of those files. The original wm.mgz file had the following dimensions: mri_info /Users/Isabelle/Desktop/wm/S08/wm.mgz Volume information for /Users/Isabelle/Desktop/wm/S08/wm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 whereas the modified wm.mgz file has the following dimensions: mri_info /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/wm.mgz Volume information for /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/wm.mgz type: MGH dimensions: 255 x 255 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -127.5, xend: 127.5 ystart: -127.5, yend: 127.5 zstart: -128.0, zend: 128.0 I am installing Freesurfer on another Mac running El Capitan to see if the problem persists. Any ideas as to what is causing the problem? Thanks, Isabelle On 8 Aug 2016, at 12:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: brain mask and T1 are not the same size (Isabelle Deschamps) -- Message: 1 Date: Mon, 8 Aug 2016 13:21:09 + From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca> Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <56102043-b30a-4e16-b1b8-8cdf75269...@ulaval.ca> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160808/c03a96e3/attachment-0001.html -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 150, Issue 11 *** 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] brain mask and T1 are not the same size
I also tried on a different computer with a different operating system (Yosemite) the manual corrections for the skull stripping and the same problem persists (dimension of the modified T1 changes to 255 x 255 x 256). Any ideas regarding how I can do these modifications for those 4 participants? Thank you in advance for your help, Isabelle * Isabelle Deschamps, Chercheure postdoctorale, Faculté de Médecine Département de réadaptation Université Laval Pavillon Ferdinand-Vandry 1050 avenue de la Médecine Québec (Québec) G1V 0A6 Centre de Recherche de l'Institut universitaire en santé mentale de Québec (CRIUMSQ) 2601, chemin de la Canardière, bureau F-2424A Québec (Québec) G1J 2G3 Téléphone : 418 663-5000 poste 6857 On Aug 5, 2016, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: TRACULA tract endpoints on cortical surface (Barbara Kreilkamp) 4. recent problems with hippocampal subfield and brainstem modules (Iglesias, Eugenio) 5. Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) (Heidi Grohn) 6. Spearman correlation in FreeSurfer (martina.papme...@puk.unibe.ch) 7. Error using LGI script despite making suggested changes to Matlab script. (Sam Mathias) 8. Re: Spearman correlation in FreeSurfer (Douglas N Greve) 9. Re: How does Optseq ___ 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] brain mask and T1 are not the same size
Can you try running simply freeview -v /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz Then save to a different file name using the "Save Volume As". Does that file have the right dimensions? Then make an edit and then "Save Volume". Does that file have the right dims? It might be a mac thing; I've been working under linux On 08/03/2016 01:05 PM, Isabelle Deschamps wrote: > I am using an iMAC with mountain lion (10.8.5). I have this version of > Freesurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > I open using a terminal Freeview: > > freeview -v > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/brainmask.mgz > \ > -f > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.white:edgecolor=yellow > > \ > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/lh.pial:edgecolor=red > > \ > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.white:edgecolor=yellow > > \ > /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/surf/rh.pial:edgecolor=red > > \ > > Then I follow these instructions > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview). > > So basically, I look for areas where the skull or meninges are > included within the pial boundary. > > I use the recon edit button, making sure that the brainmask is > highlighted (see Screen shot attached). I use the default parameters > as it has worked well for me in the past. When I am done editing the > brainmask, I save the changes using the save volume button. Then I run > the following command to regenerate the pial surface. > > recon-all -autorecon-pial -subjid S08_FS. > > Let me know if I can provide other information. I am puzzled as to why > it worked for 3/4 of the participants but it won't work for 4 of them. > > Thank you again for the help, > > Isabelle > > > Sorry, I did not see that one of the volumes was 256x256x255. I cannot > replicate here on your data using 5.3 under linux. Can you say exactly > what you do in freeview? Also, what version of FS are you using? And > what platform? > > On 3 Aug 2016, at 12:00, <freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> > wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> >> >> You can reach the person managing the list at >> freesurfer-ow...@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> >> Today's Topics: >> >> 1. Re: brain mask and T1 are not the same size (Isabelle Deschamps) >> 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) >> 3. Re: mapping error (Douglas Greve) >> 4. Re: Multiple Comparison Question for surface-based analyses >> (Douglas Greve) >> 5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki) >> 6. Re: brain mask and T1 are not the same size (Douglas N Greve) >> >> >> -- >> >> Message: 1 >> Date: Wed, 3 Aug 2016 10:50:30 + >> From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca> >> Subject: Re: [Freesurfer] brain mask and T1 are not the same size >> To: "<freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <8f31a8f6-59c6-4d12-a2a4-2ef526465...@ulaval.ca> >> Content-Type: text/plain; charset="us-ascii" >> >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/fc0fed11/attachment-0001.html >> >> -- >> >> Message: 2 >> Date: Wed, 3 Aug 2016 20:19:09 +0900 >> From: Anri WATANABE <z2aa...@koto.kpu-m.ac.jp> >> Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <caaw-jjeawc33oax6oameuect3q06ah8zyfd6nuuo32bn-eh...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Anastasia, >> >> Thank you
Re: [Freesurfer] brain mask and T1 are not the same size
enn.edu>> >> Content-Type: text/plain; charset=utf-8 >> >> Hello All, >> >> We are studying adolescents with HIV and are interested in >> frontostriatal tracts (anything from frontal cortex to >> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. >> >> Is anyone aware of DTI based atlases where these tracts are defined >> in MNI or some other standard space ? >> >> Any suggestions will be very helpful. >> >> Best >> >> Ri >> >> >> -- >> >> Message: 2 >> Date: Tue, 2 Aug 2016 12:54:01 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] Multiple Comparison Question for >> surface-based analyses >> To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <57a0d029.7020...@nmr.mgh.harvard.edu >> <http://nmr.mgh.harvard.edu>> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> I have been doing simulations similar to #1 (Eklund) using >> surface-based analysis on both thickness and fMRI. I'll prepare a report >> of the results, but the early indications are that the same effect is in >> play, though it does not look like the effects are as bad as in Eklund. >> >> For thickness analysis using applied smoothing of 5 or 10 mm FWHM, for a >> voxel-wise threshold of .001, the false positives are appropriate (ie, >> 5%). For a voxel-wise threshold of .01, the false positives is only a >> little off (about 7%); for a voxel-wise threshold of .05, the FPR is >> about 13%. If the data are not smoothed at all, then the false positive >> rates go way up. The reason appears to be the same as found in Eklund >> (ie, the autocorrelation function has a heavier-than-Gaussian tail). I >> did the analysis by randomly selecting 40 subjects from a homogeneous >> data set of 809 subjects aged 18-25. I then made two groups of 20 >> subjects each and ran a two-group test, then found clusters significant >> based on our Monte Carlo (Gaussian) simulations. I repeated this several >> thousand times. Any significant clusters were interpreted as false >> positives. These results are much better than Eklund, but Eklund was >> analyzing fMRI data. >> >> I'm still working on the fMRI data. It is much more complicated because >> the results depend on the assumed stimulus schedule (eg, 10 sec blocks >> vs 30 sec blocks) and whether a one-group or two-group anaysis is done; >> nuisance variables also play a role. At very low cluster-forming >> thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01, >> the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is >> all for an applied smoothing level of 5mm. >> >> All of these results are preliminary, so don't take them as true and >> established yet. As a reminder, you can always do a permutation test >> using mri_glmfit-sim. Eklund found that permutation did pretty well in >> most cases. >> >> doug >> >> >> On 8/2/16 12:43 AM, Ajay Kurani wrote: >>> Hello Freesurfer Experts, >>> Recently there were two article published regarding clusterwise >>> simulations for volumetric fmri analyses and potential errors for >>> underestimating clusterwise extent thresholds. >>> >>> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >>> 2) biorxiv.org/content/early/2016/07/26/065862 >>> <http://biorxiv.org/content/early/2016/07/26/065862> >>> <http://biorxiv.org/content/early/2016/07/26/065862> >>> >>> One issue pointed out from these articles seems software specific, >>> however the second issue is determining the proper clustersize. The >>> heavy-tail nature of spatial smoothness seems to be ignored and a >>> gaussian shape is generally assumed, leading to an underestimation of >>> the spatial smoothness which can affect cluster size calculations. >>> The issues are highlighted in the second article above. >>> >>> I created my own monte carlo simulation in Freesurfer for a specific >>> brain template and I wanted to find out if these concerns also apply >>> to my surface based simulations? I am not sure if it does since the >>> monte carlo tool is a GRF simulation as opposed to an analytic >>> equation, however given that these articles were highlighted very >>> recently, I wanted to ensure I am running things app
Re: [Freesurfer] brain mask and T1 are not the same size
a voxel-wise threshold of .01, the false positives is only a little off (about 7%); for a voxel-wise threshold of .05, the FPR is about 13%. If the data are not smoothed at all, then the false positive rates go way up. The reason appears to be the same as found in Eklund (ie, the autocorrelation function has a heavier-than-Gaussian tail). I did the analysis by randomly selecting 40 subjects from a homogeneous data set of 809 subjects aged 18-25. I then made two groups of 20 subjects each and ran a two-group test, then found clusters significant based on our Monte Carlo (Gaussian) simulations. I repeated this several thousand times. Any significant clusters were interpreted as false positives. These results are much better than Eklund, but Eklund was analyzing fMRI data. I'm still working on the fMRI data. It is much more complicated because the results depend on the assumed stimulus schedule (eg, 10 sec blocks vs 30 sec blocks) and whether a one-group or two-group anaysis is done; nuisance variables also play a role. At very low cluster-forming thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01, the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is all for an applied smoothing level of 5mm. All of these results are preliminary, so don't take them as true and established yet. As a reminder, you can always do a permutation test using mri_glmfit-sim. Eklund found that permutation did pretty well in most cases. doug On 8/2/16 12:43 AM, Ajay Kurani wrote: Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 <http://biorxiv.org/content/early/2016/07/26/065862> One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Message: 3 Date: Tue, 2 Aug 2016 13:18:09 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57A0D5D1.20301@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed The voxel size and dimensions of all three volumes are the same: 256^3 and 1mm^3. Why do you think they are not? On 08/02/2016 09:17 AM, Isabelle Deschamps wrote: Yes, of course. The upload is now active. Thank you again for your help, Isabelle On 2 Aug 2016, at 08:55, freesurfer-requ...@nmr.mgh.harvard.edu <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Re: [Freesurfer] brain mask and T1 are not the same size ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Message: 4 Date: Tue, 2 Aug 2016 14:17:28 -0400 From: Jordan Chad <jc...@research.baycrest.org> Subject: [Freesurfer] Save Overlay via Command Line To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CA+FdjQX9T0cr50M4awGdW0YJHM3n32FrFcQ9AvGM_+=vmb1...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am trying to perform between-subject statistics on cortical DTI data in certain ROIs. I can do this by overlaying the DTI data on the surfaces on tksurfer, load and mask the label with the ROI, and then go to File -> Save Overlay. After doing this for all subjects I can perform statistics on the output files. However, it is not practical to do this for al
Re: [Freesurfer] brain mask and T1 are not the same size
The voxel size and dimensions of all three volumes are the same: 256^3 and 1mm^3. Why do you think they are not? On 08/02/2016 09:17 AM, Isabelle Deschamps wrote: > Yes, of course. The upload is now active. > > Thank you again for your help, > > Isabelle > On 2 Aug 2016, at 08:55, freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > >> Re: [Freesurfer] brain mask and T1 are not the same size > > > > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] brain mask and T1 are not the same size
Yes, of course. The upload is now active. Thank you again for your help, Isabelle On 2 Aug 2016, at 08:55, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Re: [Freesurfer] brain mask and T1 are not the same size ___ 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] brain mask and T1 are not the same size
So you're saying that the dimension changed after you ran freeview and saved the volume? Can you replicate it? ie, if you make a copy of the brainmask.mgz, then edit the copy, does it do the same thing every time you make a copy and edit it? Yes it does. I tried multiple time your suggestion (copying brain mask) and the same error happens. I tried erasing different brain areas of the brain mask to understand the source of the problem, and for these 4 participants it does not seem to matter what I erase or not. The dimensions change. Thank you for your help, Isabelle Isabelle On Jul 30, 2016, at 11:23 AM, "freesurfer-requ...@nmr.mgh.harvard.edu" <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Fwd: question about volume of mask (Dorsa Haji Ghaffari) 2. brain mask and T1 are not the same size (Isabelle Deschamps) 3. Re: error during longitudinal -long stream (Jinsong Tang) 4. Research Assistants needed for longitudinal brain development study at Boston Children's Hospital (Gaab, Nadine) 5. Re: error during longitudinal -long stream (Martin Reuter) 6. MNI coordinates of all the vertices of fsaverage (Sabin Khadka) 7. Running Retinotopy in FSFAST, Design Matrix has Empty Regressors (Taylor, Johnmark) 8. mri_normalize, 110 is too dark (tvg[fs]) 9. Re: brain mask and T1 are not the same size (Douglas Greve) 10. Re: mri_normalize, 110 is too dark (Bruce Fischl) 11. Where are time series from adjusted (post selxavg3) ROIs (ERIK JAHNER) 12. Re: significance overlay in freeview (Caroline Beelen) 13. Running recon-all with T1 and FLAIR (Silas) 14. Re: error during longitudinal -long stream (Jinsong Tang) -- Message: 1 Date: Fri, 29 Jul 2016 12:08:43 -0400 From: Dorsa Haji Ghaffari <gh...@umich.edu> Subject: [Freesurfer] Fwd: question about volume of mask To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAAe2pvAtEfwUj6=7G+qe8jknxm23sj8pyf4zncfkbshxotn...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Bruce, I was able to reslice the thalamus mask correctly, but when I measure the volume of the resliced thalamus, is not the same as the original thalamus. I was wondering why that is happening and which volume is more accurate. I appreciate any suggestions. I have attached both masks. Also can you tell me how to measure the volume of the resliced thalamus in Freesurfer? Thank you Dorsa -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160729/c9ee2c24/attachment-0001.html -- next part -- A non-text attachment was scrubbed... Name: reslicedgmthalamus.nii.gz Type: application/x-gzip Size: 194056 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160729/c9ee2c24/attachment-0002.gz -- next part -- A non-text attachment was scrubbed... Name: gmthalamus.nii.gz Type: application/x-gzip Size: 67272 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160729/c9ee2c24/attachment-0003.gz -- Message: 2 Date: Fri, 29 Jul 2016 16:09:31 + From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca> Subject: [Freesurfer] brain mask and T1 are not the same size To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <23b16dc7-f62a-4b8b-99da-eddad20a1...@ulaval.ca> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160729/c735bc24/attachment-0001.html -- Message: 3 Date: Fri, 29 Jul 2016 09:26:58 -0700 From: Jinsong Tang <tangjinson...@gmail.com> Subject: Re: [Freesurfer] error during longitudinal -long stream To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CADf-At00N-cyZYTLt0z7EvK1Hk4b=cyasjvmde3rg7zsm_r...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Martin, I checked all data are completed except the link to fsaverage, lh.EC_average and rh.EC_average. I run one analysis from the terminal. it works. if I run multiple analysis at the same time, it
Re: [Freesurfer] brain mask and T1 are not the same size
So you're saying that the dimension changed after you ran freeview and saved the volume? Can you replicate it? ie, if you make a copy of the brainmask.mgz, then edit the copy, does it do the same thing every time you make a copy and edit it? On 7/29/16 12:09 PM, Isabelle Deschamps wrote: Dear FreeSurfer experts, I am trying to fix the skull strip manually for a group of participants. For all participants except 4, I get an error when running recon-all -autorecon-pial -subjid S07_FS, after editing manually in Freeview the brainmask. In freeview, I followed the instruction for Edits to the brainmask (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon) I open freeview using this command on my participant's data: *freeview -v pial_edits_before/mri/brainmask.mgz \* *-f pial_edits_before/surf/lh.white:edgecolor=yellow \* *pial_edits_before/surf/lh.pial:edgecolor=red pial_edits_before/surf/rh.white:edgecolor=yellow \* *pial_edits_before/surf/rh.pial:edgecolor=red * Then, I follow these instructions, which are on the website. *To fix this type of error you can simply edit away the offending voxels from the brainmask.mgz volume. To do this you will need to select the edit voxels tool and set the brush to a size and shape comfortable for you. A circle brush of radius 2 works well for this edit. Then you can simply use the shift key and your mouse button to erase the voxels in the brainmask.mgz, or you can set the brush value to 1 (so that the edits can be detected if you decide to run "recon-all -show-edits") and simple draw over the voxels you want to disappear.* Then I save the brainmask volume using the save volume button. When running *recon-all -autorecon-pial -subjid S07_FS* to correct the pial surface, I get the following error: ERROR: dimension mismatch between source and mask The source of the problem is the the brainmask, in which one of the dimensions is no longer 256. It is either 255 or 254. Prior the modifications, the brainmask and the T1 had the same dimensions 256^3. Following the brainmask edits, one dimension (it varies for the 4 problematic participants) is no longer 256. I do not understand why for all participants except 4, the brainmask edits worked. I followed the exact same procedure for all participants. Any ideas or suggestions? Thank you in advance for the help, Isabelle ___ 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] brain mask and T1 are not the same size
Dear FreeSurfer experts, I am trying to fix the skull strip manually for a group of participants. For all participants except 4, I get an error when running recon-all -autorecon-pial -subjid S07_FS, after editing manually in Freeview the brainmask. In freeview, I followed the instruction for Edits to the brainmask (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon) I open freeview using this command on my participant's data: freeview -v pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red Then, I follow these instructions, which are on the website. To fix this type of error you can simply edit away the offending voxels from the brainmask.mgz volume. To do this you will need to select the edit voxels tool and set the brush to a size and shape comfortable for you. A circle brush of radius 2 works well for this edit. Then you can simply use the shift key and your mouse button to erase the voxels in the brainmask.mgz, or you can set the brush value to 1 (so that the edits can be detected if you decide to run "recon-all -show-edits") and simple draw over the voxels you want to disappear. Then I save the brainmask volume using the save volume button. When running recon-all -autorecon-pial -subjid S07_FS to correct the pial surface, I get the following error: ERROR: dimension mismatch between source and mask The source of the problem is the the brainmask, in which one of the dimensions is no longer 256. It is either 255 or 254. Prior the modifications, the brainmask and the T1 had the same dimensions 256^3. Following the brainmask edits, one dimension (it varies for the 4 problematic participants) is no longer 256. I do not understand why for all participants except 4, the brainmask edits worked. I followed the exact same procedure for all participants. Any ideas or suggestions? Thank you in advance for the help, Isabelle ___ 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.
