Re: [Freesurfer] Viewing Control Points
yes, that will prevent it I believe. Or you can load them in freeview from the interface (I believe they are a type of pointset in freeview) On Thu, 27 Oct 2011, Matt Glasser wrote: Hi Bruce, That didn't happen, but perhaps because I loaded the volume with -f instead of the more standard way. I'll try it again. Thanks, Matt. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, October 27, 2011 12:53 PM To: Matt Glasser Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing Control Points Hi Matt they will be loaded by default in tkmedit when you load any volume if the file subject/tmp/control.dat exists. cheers Bruce On Thu, 27 Oct 2011, Matt Glasser wrote: Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt. 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] Viewing Control Points
Hi Bruce, That didn't happen, but perhaps because I loaded the volume with -f instead of the more standard way. I'll try it again. Thanks, Matt. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, October 27, 2011 12:53 PM To: Matt Glasser Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing Control Points Hi Matt they will be loaded by default in tkmedit when you load any volume if the file subject/tmp/control.dat exists. cheers Bruce On Thu, 27 Oct 2011, Matt Glasser wrote: > > Hi, > > > > Is it possible to view control points (in control.dat), that you already > created? If so, how do you do it? > > > > Thanks, > > Matt. > > > 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] Viewing Control Points
Hi Matt they will be loaded by default in tkmedit when you load any volume if the file subject/tmp/control.dat exists. cheers Bruce On Thu, 27 Oct 2011, Matt Glasser wrote: Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt. ___ 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] Viewing Control Points
Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt. ___ 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] FW: Question on mris_pmake
Regarding my first question in my previous post below, the same error occurs even when I run my script (containing many repetition of mris_pmake command) on only one terminal window. From: Jungwon Ryu [mailto:rjung...@snu.ac.kr] Sent: Tuesday, October 25, 2011 8:11 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Question on mris_pmake Hi, I'm trying to get distances on a cortical surface between sets of voxels in visual areas and I have two questions; 1) I have the following error message so often; === System error: Address already in use Fatal error encountered. SSocket `Unnamed SSocket_UDP_receive' (id: 0) Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive Problem binding to socket 1701 Error returned from system: Address already in use Throwing exception to (this) with code 1 terminate called after throwing an instance of 'c_SSocket*' runSh_Ori_1_02_01.sh: line 5789: 93334 Abort trap mris_pmake --subject JR20110819 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:907,endVertex:731 >> result_Ori_1_02_01.txt === I have around 10,000 voxel pairs to run mris_pmake( ) command. Since I have to call mris_pmake( ) so many times (one pair by one pair), I splitted the whole list of voxel pairs into four script files, containing many mris_pmake commands with 2,500 voxel pairs as arguments, then I ran scripts with four terminal windows saparately to parallelize the processing. All script files are located in the same diretory. Then I had the message as above. What might be the problem? (It seems as if multiple terminal instances share the socket port number) 2) How can I get interhemispheric distances between visual areas across hemispheres? Ryu PhD student Department of Brain and Cognitive Sciences, Seoul National University, Korea ___ 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] cortical thickness asymmetries
We have mentioned this in: "Use of SVM Methods with Surface-Based Cortical and Volumetric Subcortical Measurements to Detect Alzheimer's Disease" You can find the PDF in the FreeSurfer page: http://surfer.nmr.mgh.harvard.edu/ftp/articles/Oliveira_JAD2010.pdf I don't have a good explanation though. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Oct 27, 2011 at 10:03, Bruce Fischl wrote: > not that I know of > > Bruce > On Thu, 27 Oct 2011, Irene Altarelli wrote: > > > Dear Freesurfer experts, > > > > have cortical thickness asymmetries ever been looked at using Destrieux > > parcellation scheme, either in adults or (even better) in children? > > > > Thanks! > > Irene > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical thickness asymmetries
not that I know of Bruce On Thu, 27 Oct 2011, Irene Altarelli wrote: > Dear Freesurfer experts, > > have cortical thickness asymmetries ever been looked at using Destrieux > parcellation scheme, either in adults or (even better) in children? > > Thanks! > Irene > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Segmentation error?
total brain volume would be a more conservative normalization - it would test the hypothesis that some brain regions are atrophying faster than average. cheers Bruce On Thu, 27 Oct 2011, Gergely Orsi wrote: Yes. This was our guess also, the problem is that these subject were scanned with an old MPRAGE sequence that has only 160 slices and 0.94mm slice thickness, thus it does not provide full brain coverage, part of the cerebellum is missing for the big headed subjects. That is the main reason for the cerebellum cutoff. Is it a good idea to normalize the brain volumes (total gray m., total white m., ventricles, CSF) with brain mask volume instead of ICV? We just want to evaluate these 7 subjects, they have 2 time points (24 hours post injury and 3 months later) and want to compensate for different skull size. The volume values will be correlated with other parameters like MD, FA, LI, clinical scores, etc. They were all measured with the same non-Freesurfer optimized MPRAGE sequence (TR:1900ms, TE:3,41ms, FOV: 240mm, FOV Phase:87,5%, slice thickness: 0,94mm, number of slices :160, phase encoding direction: R->L, TI:900ms, flip angle:9° matrix:256×256, bandwith:180Hz/pixel, resolution: 0,94×0,94×0,94mm.) Can you suggest any other measured parameter that we can use to normalize the volumes? One more question, how can we assess the total left and right hemisphere' volume? Thank you very much. Gergo 2011/10/25 Bruce Fischl I think your acquisition is cutting off some cerebellum, and in any case has a very steep intensity drop off in the cerebellum and brainstem. Is it slab selective in that direction? You might try increasing the size of the slab or lengthening your slab-select pulse, or including some oversampling in that direction. On Tue, 25 Oct 2011, Gergely Orsi wrote: SZEMAN2.tar.gz have just been uploaded. Thank you Gergo 2011/10/25 Gergely Orsi Yes of course, just a minute. 2011/10/25 Bruce Fischl I meant canyou tar and gzip the subject and ftp it to us On Tue, 25 Oct 2011, Gergely Orsi wrote: Here you are: # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab /home/kutato/freesurfer/ASegStatsLUT.txt # sysname Linux # hostname kutato16 # machine x86_64 # user kutato16 # anatomy_type volume # # SUBJECTS_DIR /home/kutato/freesurfer/subjects # subjectname SZEMAN2 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2011/09/30 14:48:41 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 964476.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 986721, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2011/09/30 21:17:55 # ColorTable /home/kutato/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2009/08/11 14:24:37 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2011/09/30 15:23:28 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2011/09/30 15:23:28 # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500 # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000 # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500 # ExcludeSegId 0 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume
[Freesurfer] cortical thickness asymmetries
Dear Freesurfer experts, have cortical thickness asymmetries ever been looked at using Destrieux parcellation scheme, either in adults or (even better) in children? Thanks! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Segmentation error?
Yes. This was our guess also, the problem is that these subject were scanned with an old MPRAGE sequence that has only 160 slices and 0.94mm slice thickness, thus it does not provide full brain coverage, part of the cerebellum is missing for the big headed subjects. That is the main reason for the cerebellum cutoff. Is it a good idea to normalize the brain volumes (total gray m., total white m., ventricles, CSF) with brain mask volume instead of ICV? We just want to evaluate these 7 subjects, they have 2 time points (24 hours post injury and 3 months later) and want to compensate for different skull size. The volume values will be correlated with other parameters like MD, FA, LI, clinical scores, etc. They were all measured with the same non-Freesurfer optimized MPRAGE sequence (TR:1900ms, TE:3,41ms, FOV: 240mm, FOV Phase:87,5%, slice thickness: 0,94mm, number of slices :160, phase encoding direction: R->L, TI:900ms, flip angle:9° matrix:256×256, bandwith:180Hz/pixel, resolution: 0,94×0,94×0,94mm.) Can you suggest any other measured parameter that we can use to normalize the volumes? One more question, how can we assess the total left and right hemisphere' volume? Thank you very much. Gergo 2011/10/25 Bruce Fischl > I think your acquisition is cutting off some cerebellum, and in any case > has a very steep intensity drop off in the cerebellum and brainstem. Is it > slab selective in that direction? You might try increasing the size of the > slab or lengthening your slab-select pulse, or including some oversampling > in that direction. > > > On Tue, 25 Oct 2011, Gergely Orsi wrote: > > SZEMAN2.tar.gz have just been uploaded. >> >> Thank you >> >> Gergo >> >> 2011/10/25 Gergely Orsi >> Yes of course, just a minute. >> >> >> 2011/10/25 Bruce Fischl >> I meant canyou tar and gzip the subject and ftp it to us >> >> On Tue, 25 Oct 2011, Gergely Orsi wrote: >> >> Here you are: >> >> # Title Segmentation Statistics >> # >> # generating_program mri_segstats >> # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 >> nicks Exp $ >> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv >> mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask >> mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm >> --in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab >> /home/kutato/freesurfer/**ASegStatsLUT.txt >> # sysname Linux >> # hostname kutato16 >> # machine x86_64 >> # user kutato16 >> # anatomy_type volume >> # >> # SUBJECTS_DIR /home/kutato/freesurfer/**subjects >> # subjectname SZEMAN2 >> # BrainMaskFile mri/brainmask.mgz >> # BrainMaskFileTimeStamp 2011/09/30 14:48:41 >> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1460346, >> unitless >> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, >> mm^3 >> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation >> Volume >> Without Ventricles, 964476.00, mm^3 >> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> 986721, unitless >> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 986721.00, >> mm^3 >> # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, >> mm^3 >> # SegVolFile mri/aseg.mgz >> # SegVolFileTimeStamp 2011/09/30 21:17:55 >> # ColorTable /home/kutato/freesurfer/**ASegStatsLUT.txt >> # ColorTableTimeStamp 2009/08/11 14:24:37 >> # InVolFile mri/norm.mgz >> # InVolFileTimeStamp 2011/09/30 15:23:28 >> # InVolFrame 0 >> # PVVolFile mri/norm.mgz >> # PVVolFileTimeStamp 2011/09/30 15:23:28 >> # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500 >> # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000 >> # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500 >> # ExcludeSegId 0 >> # VoxelVolume_mm3 1 >> # TableCol 1 ColHeader Index >> # TableCol 1 FieldName Index >> # TableCol 1 Units NA >> # TableCol 2 ColHeader SegId >> # TableCol 2 FieldName Segmentation Id >> # TableCol 2 Units NA >> # TableCol 3 ColHeader NVoxels >> # TableCol 3 FieldName Number of Voxels >> # TableCol 3 Units unitless >> # TableCol 4 ColHeader Volume_mm3 >> # TableCol 4 FieldName Volume >> # TableCol 4 Units mm^3 >> # TableCol 5 ColHeader StructName >> # TableCol 5 FieldName Structure Name >> # TableCol 5 Units NA >> # TableCol 6 ColHeader normMean >> # TableCol 6 FieldName Intensity normMean >> # TableCol 6 Units MR >> # TableCol 7 ColHeader normStdDev >> # TableCol 7 FieldName Itensity normStdDev >> # TableCol 7 Units MR >> # TableCol 8 ColHeader normMin >> # TableCol 8
