Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 07 Aug '13

07 Aug '13

Hi Bruce, Thanks very much for the explanation. According to your suggestion, I think maybe I should try to figure it out with a 2D fast marching process. I could extract it to a 2 dimension matrix by matlab with FreeSurfer package, right? Best, Yunxin 2013/8/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Yunxin > > could you cc the list so that others can answer? I don't think you will be > able to get a reasonable surface out of a discretized 256*3 volume for the > pial surface. There are many, many places where the pial surface comes > within a fraction of a mm of itself that you will not be able to represent. > > cheers > Bruce > > > On Tue, 6 Aug 2013, Yunxin Wang wrote: > > Hi Bruce, >> Thanks for your response. Actually I want to use the fast marching toolbox >> to further analyze the pial surface that FreeSurfer has reconstructed >> automatically, but according to the procedure only the pial surface will >> be >> used for fast marching process and I found out the input file of fast >> marching is a 256*256*256 matlab file which I could just load in matlab >> but >> couldn't see any detail. Do you think I can use the freesurfer_read_surf >> function in matlab to transfer the surface? >> >> Best, >> Yunxin >> >> >> 2013/8/5 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Yunxin >> >> the surface lives in a continuum and is 2D. Do you mean filling >> the space between the ?h.white and ?h.pial surfaces? We do that >> as part of recon-all and create ribbon volumes in the mri dir >> cheers >> Bruce >> >> >> On Mon, 5 Aug 2013, Yunxin Wang wrote: >> >> Hi dear all, >> I'm new here and I've a simple question that how >> could I transfer the reconstructed pial surface >> file(like lh.pial) into a >> 256*256*256 matlab matrix used in later fast >> marching process? >> >> Any suggestion will be appreciated! >> Thank guys. >> >> Best, >> Yunxin Wang >> >> >> >> >> >> >> 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<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. >> >> >> >>

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Postdoctoral position: the brain connectome in twins populations
by Katell Mevel 07 Aug '13

07 Aug '13

Dear brain imaging fellows, One post-doc position is available in our group, the deadline is 30-08-2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND) (www.ki.se/kind) KIND is a competence center for research, development and education within the area of developmental psychopathology. The center is established in collaboration between Karolinska Institutet and Stockholm County Council, and aims at improving clinical practice, generating basic research, and spreading new knowledge to stakeholders. The Roots of Autism Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins being discordant for autism spectrum disorder and other neurodevelopmental disorders, e.g. ADHD. For the first time ever, twins are examined on multiple levels, among them functional and structural neuroimaging using MRI. Scanning is performed in the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750), and more than 45 pairs have now been examined. *** Duties As a post-doc, you will be mainly responsible for the acquisition and analyses of the multimodal neuroimaging data. This includes DTI, resting-state fMRI and structural T1, to be combined according to a brain connectome approach. This work will be done in close collaboration with the department of Clinical Neuroscience. The position also includes several other responsibilities, e.g. coordination of the neuroimaging works at KIND, involvement in international collaborations, administrative tasks, grant application and article writing. All the details about this position can be found here:https://ki.mynetworkglobal.com/en/what:job/jobID:24397/where:4/ Applications should be submitted here:https://ki.mynetworkglobal.com/what:login/jobID:24397/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best Regards, Katell MEVEL for KIND ________________________________ Katell Mevel | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B | 113 30 Stockholm +46 (0)8 514 52706 | +46 (0)721 980 350 katell.mevel(a)ki.se | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130><http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ______________________________________ Karolinska Institutet – a medical university

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job offer
by Anton Eberharter 07 Aug '13

07 Aug '13

Please post the following job offer, see attachment. Thanks in advance, Anton Eberharter ===================================== PD Dr. Anton Eberharter Lab Manager & Dozent Physiologische Chemie / Medizinische Fakultät Ludwig Maximilians Universität München Butenandtstr. 5B 81377 München Tel.: 089 2180 77096 anton.eberharter(a)med.lmu.de<mailto:anton.eberharter@med.lmu.de> www.ladurnerlab.de<http://www.ladurnerlab.de/> =====================================

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Fwd: How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 06 Aug '13

06 Aug '13

---------- Forwarded message ---------- From: Yunxin Wang <yunxinwang(a)gmail.com> Date: 2013/8/6 Subject: Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thanks for your response. Actually I want to use the fast marching toolbox to further analyze the pial surface that FreeSurfer has reconstructed automatically, but according to the procedure only the pial surface will be used for fast marching process and I found out the input file of fast marching is a 256*256*256 matlab file which I could just load in matlab but couldn't see any detail. Do you think I can use the *freesurfer_read_surf*function in matlab to transfer the surface? Best, Yunxin 2013/8/5 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Yunxin > > the surface lives in a continuum and is 2D. Do you mean filling the space > between the ?h.white and ?h.pial surfaces? We do that as part of recon-all > and create ribbon volumes in the mri dir > cheers > Bruce > > > > On Mon, 5 Aug 2013, Yunxin Wang wrote: > > Hi dear all, >> I'm new here and I've a simple question that how could I transfer the >> reconstructed pial surface file(like lh.pial) into a >> 256*256*256 matlab matrix used in later fast marching process? >> >> Any suggestion will be appreciated! >> Thank guys. >> >> Best, >> Yunxin Wang >> >> >> >> >> > > 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<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. >

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How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 06 Aug '13

06 Aug '13

Hi dear all, I'm new here and I've a simple question that how could I transfer the reconstructed pial surface file(like lh.pial) into a 256*256*256 matlab matrix used in later fast marching process? Any suggestion will be appreciated! Thank guys. Best, Yunxin Wang

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Fwd: fsaverage
by Fco. Javier Román 06 Aug '13

06 Aug '13

Hi Bruce, thanks so much!! Do you know some web (or maybe you cant send to me) to obtained the files of the version 4.5.0? Thanks!! FJ 2013/8/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Franciso, > > I think that we made some small mods to the spherical registration in that > time to make it more robust, so things probably did change > > cheers > Bruce > > > On Tue, 6 Aug 2013, Fco. Javier Román wrote: > > Hello! >> I want to know if there are any change in the files of the folder >> fsaverage >> in the different versions of freesurfer. Specifically, I'm interested in >> know if the files lh.pial_avg and rh.pial_avg are the same in the versions >> v4.5.0 and v5.3.0 >> >> Many thanks in advance, >> >> Best, >> -- >> Francisco Javier Román >> >> >> > > 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<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. > -- Francisco Javier Román -- Francisco Javier Román

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fsaverage
by Fco. Javier Román 06 Aug '13

06 Aug '13

Hello! I want to know if there are any change in the files of the folder *fsaverage * in the different versions of freesurfer. Specifically, I'm interested in know if the files lh.pial_avg and rh.pial_avg are the same in the versions v4.5.0 and v5.3.0 Many thanks in advance, Best, -- Francisco Javier Román

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Best way to generate Complete Stats Table
by Salil Soman 06 Aug '13

06 Aug '13

Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns). Best wishes, Sla

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Re: [Freesurfer] Fwd: infant atlas segmentation
by Douglas N Greve 06 Aug '13

06 Aug '13

I think I gave you the wrong command line for mri_label2vol. Try added --invertmtx to the command line. Sorry for the wild goose chase. doug On 08/06/2013 04:00 PM, Mark Plantz wrote: > The bbregister output looks like a typical intensity volume [attached]. > > Out of curiosity, I ran mri_label2vol with a different segmentation > volume (the aparc+aseg default). It looks like the images are not > inverted, but the sagittal has been switched with the coronal view. Is > it possible that my version of mri_label2mri has a bug? > > > > > On Tue, Aug 6, 2013 at 2:46 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > What happens if you load the output of bbregister? > > > On 08/06/2013 03:30 PM, Mark Plantz wrote: > > The output of bbregister is actually fine. It seems like the > inversion happens after mri_label2vol is run. I am currently > viewing in FreeView, but the tkmedit command is: > > tkmedit CMH-8169 001.mgz -segmentation > /Applications/freesurfer/subjects/CMH-8169/mri/output.mgz > > LoadSegmentationVolume main > /Applications/freesurfer/subjects/CMH-8169/mri/output.mgz > /Applications/freesurfer/FreeSurferColorLUT.txt > Reading /Applications/freesurfer/tktools/tkm_common.tcl > Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > > > > > On Tue, Aug 6, 2013 at 12:59 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > That all looks right, and the number of labels = 0 is not a > problem. Is the output of bbregister flipped? What is your > tkmedit > command? > doug > > > On 08/06/2013 10:13 AM, Mark Plantz wrote: > > I think that the registration turned out ok [well it isn't > upside down]. I attached a few screenshots. > > My bbregister command is: > > *bbregister --s CMH-8169 --mov > > /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/seg.mgz > --init-fsl --reg > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/register.dat > --t1 --o > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/output.mgz* > * > > * > Subsequently, my mri_label2vol command is: > > *ingvalsons-imac:~ IngvalsonLab$ mri_label2vol --seg > > /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/seg.mgz > --temp > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/output.mgz > --reg > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/register.dat > --o /Users/IngvalsonLab/Desktop/output.mgz * > > > Number of labels: 0 > Annot File: (null) > Template Volume: > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/output.mgz > Outut Volume: /Users/IngvalsonLab/Desktop/output.mgz > Registration File: > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/register.dat > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /Applications/freesurfer/subjects > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 > greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0 > Loading registration from > > /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-8169/bbregister/register.dat > RegMat: -------- > -0.994 -0.098 0.042 0.715; > 0.043 -0.001 0.999 -14.682; > 0.097 -0.995 -0.005 2.026; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > 0.994 0.098 -0.042 127.285; > -0.097 0.995 0.005 125.974; > 0.043 -0.001 0.999 113.318; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > ASeg2Vol: Sorting > ASeg2Vol: Mapping > ASeg2Vol: Reverse Map > nmisses = 9739499 (73560 filled) > ASeg2Vol: done > ingvalsons-imac:~ IngvalsonLab$ > > > Is it significant that number of labels = 0? Or is that > because I am using a segmentation volume instead of an > actual > .label file? > > Other than that, I cannot seem to determine why the output > images would be inverted by 180 degrees. > > Thank you in advance > MP > > > > > On Mon, Aug 5, 2013 at 4:26 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > did you look at the registration with tkregister2? > When > bbregister > finished, it would have printed out the command > line to > run (it is > also at the end of the log file). If that looks > ok, please > send > your bbregister command. > doug > > > On 8/5/13 1:47 PM, Mark Plantz wrote: > > Thanks Doug. mri_label2vol worked well, except it > looks like all > of the files are inverted by 90 degrees. They > appear > inverted in > both tkmedit and 'FreeView.' I read that > inversions > are common in > "fslview" but not in tkmedit. Any idea what > could be > causing this > problem? > > My command line is: > > *mri_label2vol --seg > > > /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/seg.mgz > --temp > /Users/IngvalsonLab/Desktop/temp.mgz --o > seg_new.mgz --reg > register.dat* > * > > * > I didn't encounter any errors with > mri_label2vol nor > bbregister > [which was used to generate register.dat and > temp.mgz]. > > Any ideas what could be causing this problem? > > I can attach more images if this one doesn't > portray the > inversion well. > > Thanks a lot > > MP > > > On Mon, Aug 5, 2013 at 10:12 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > The file that you pass it with the --reg > option is the > registration file (eg, --reg > register.dat). This > can be used > for input to mri_vol2vol or mri_label2vol. > mri_label2vol is > appropriate for a segmetation > > doug > > > > On 8/5/13 10:22 AM, Mark Plantz wrote: > > Thank you. Do you know how to access the > transform that is > outputted by bbregister. I am just > obtaining > an output > volume <volume.mgz>>? > > > On Thu, Aug 1, 2013 at 3:56 PM, Bruce > Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > Hi Mark > > you can use the transform that > bbregister > outputs and > give it to mri_convert with -at > <transform > name> > > cheers > > Bruce > > > On Thu, 1 Aug 2013, Mark Plantz wrote: > > One last question: Is there > any flag I > can use with > 'bbregister' that > prevents the labels from > changing in > my segmentation > volume? This is > occuring because the volume > that I am > moving has > labels. For some reason, > the labels change ever so > slightly in > the output file. > > > On Thu, Aug 1, 2013 at 2:28 > PM, Bruce > Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > wrote: > glad it worked out > Bruce > On Thu, 1 Aug 2013, Mark > Plantz > wrote: > > Just as an update, it > turns out that my > segmentation > volume had been > slightly altered > during > the conversion > from .nii to > .mgz. I completely > forgot to use the -rt > nearest flag to > prevent the > labels from becoming > distorted. That is > why the > segmentation > looked so > fuzzy with various > regions > labeled incorrectly. > Apparently, I should check > the basics before > overcomplicating the problem, > haha. Thanks for > the help > everyone! > > > On Thu, Aug 1, 2013 at > 9:36 AM, Mark Plantz > <markplantz2016(a)u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>>>> wrote: > Sounds good. I also > just realized > that the > segmentation values > are varying from > 0-255, which > makes me think > that the file is > only > designed for the > grayscale/heat/etc. > settings [where 0 is > darkest regions and > 255 is > brightest regions]. > Is that a valid > assumption? Also, if this is > the case, > would > it be impossible to > create a .gca file using > mri_ca_train with > these files? > Thanks for the help. > > MP > > > On Wed, Jul 31, > 2013 at > 8:43 PM, Douglas > Greve > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Just make > sure that > you create a > new file and > do not > repeat index numbers. > > > On 7/31/13 > 2:02 PM, > Mark Plantz wrote: > That makes > sense. > Wouldn't that > cause there to > be > some overlap > between > different > regions, since > the > same index > #'s used > by the two > programs > (FreeSurfer > & MRIcro) correspond > to different > brain > regions? > > > On Tue, Jul 30, > 2013 at > 12:50 PM, > Douglas Greve > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > for every > line in > that file, you > will need to > create a line in the > new LUT, > something like > > > 8 > Frontal_Mid_R 0 > 255 0 0 > > This will > make the > right mid > frontal green = > (0,255,0) > > > > > On 7/30/13 > 9:55 AM, > Mark Plantz wrote: > Hmm, so I > received > the text part > of the > LUT. Looks > like this > is completely > different from the segmented > regions > that we > would want. > [attached]. Can't > seem to > understand > how this text file > could be related to > the default > FreeSurfer LUT. It looks like the > labeling for an AAL > map. This probably > wont' work will it? > - Mark > > > On Tue, Jul 30, > 2013 at > 8:47 AM, Bruce > Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > the UNC one? > No, you > should ask > them > On Tue, 30 > Jul 2013, > Mark Plantz > wrote: > > > > ---------- Forwarded message > ---------- > From: Mark > Plantz > <markplantz2016(a)u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>>>> > > Date: Tue, > Jul 30, > 2013 at > 8:39 AM > Subject: Re: > [Freesurfer] > infant atlas > segmentation > To: Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > > Just opened > up the > default > FreeSurferColorLUT.txt file. > So it looks > like all > I have to > change is > the #No. > column of the file, > to match > the ones in the > other LUT used. > I actually just > received the > MRIcro .lut file > from the > UNC group. > [attached] > > Hopefully this will help > with the > conversion. > However, I still have to > figure out how to > open the > file. Any ideas? > > > > > On Tue, Jul > 30, 2013 > at 8:25 > AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > wrote: > Hi Mark > > creating a FreeSurfer > LUT really isn't > that hard. > Have you > looked at our standard > one? Probably we > have the > names you > already want and you > just need to > change our > indices to match > the ones in your > segmentation file (and save > it as a > different > LUT) > > cheers > Bruce > > On Tue, 30 Jul > 2013, > Mark Plantz > wrote: > > Turns out that > the files > had been > labeled > using a > color LUT in a > program > called MRIcro. I > am now > installing this > program > simply to access > the LUT. > Will it be as > simple as exchanging the > index values > from this LUT to > a > custom LUT in > FreeSurfer? > > > On Tue, Jul 30, > 2013 at > 12:35 AM, > Douglas > Greve > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > The > problem is that you > need to > create a > completely new > LUT. The > labels > that get > displayed > with the > standard > LUT are going to > be > totally > random with respect > to what > they > should display. > > On 7/29/13 > 2:20 PM, > Mark Plantz > wrote: > Hi Doug, > Thanks for the > reply. I will > definitely go > into > the LUT and > change those > values to some specific > region. My main > concern is > that I think all > of these > "out of bounds" > labels are > the > symptoms of some > larger problem. The > segmentation > looks very > strange as > compared to a typical > segmentation (i.e. > an > 'aseg.mgz' > file). In fact, the > segmentation appears > to be > labeling > "left-<region" in the right > hemisphere. > Have you seen a > segmentation > file that > looks like the > once I > attached before? > I > am used to > seeing segmentation > files > such as the one > attached to > this e-mail. > > - Mark > > > On Mon, Jul 29, > 2013 at > 12:28 PM, > Douglas > Greve > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > Mark, the > only thing > that is wrong > with the > out of > bounds > regions is that they > are not > represented in > the LUT. > Once you add > an index > corresponding > to the > index of > the > segmentation to > the LUT, > it will > not > show up as > "out of > bounds". The > brain > mask has > nothing to > do with it. > best > doug > > > > On 7/29/13 > 12:50 PM, Mark > Plantz wrote: > Sorry > about that. I > received the > manual > > segmentations from > aUNCmedicalgroup<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-in > fan > t-0-1-2 > -atla > ses>. I > actually asked the main > researcher > about the > out of bounds > regions. He > thinks > that as > long as the > segmented file > lines up > with the > input volumes, a few > out of > bounds > regions > might be OK. > However, these > seg > volumes > look very > different > from a > typical > .aseg > volume that I am used to > seeing after > recon-all > is run. > Maybe the > segmentation is simply > incompatible with > FreeSurfer? > > Thanks for the > help. These files are a > nightmare! > > - MP > > > On Mon, Jul 29, > 2013 at > 11:40 AM, Bruce > Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > wrote: > can you cc > the list please? > Maybe we > should > start over. Where > did you > get the > manual > segmentations from? > > On Mon, 29 > Jul 2013, Mark > Plantz wrote: > > Ahh, > right. So it looks like > the > red regions > appear to be > > averaged around 248. > I am > not > sure why > that is the > case > or if it has > any > significance. I attached > a > screen shot for > > reference. > > > On > Mon, Jul 29, > 2013 at > > 11:29 AM, Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > wrote: > > it isn't a > > registration file. You > > should just specify > it as a > > volume on the freeview > > command line, the > same as > > brainmask.mgz > > > On Mon, 29 > Jul 2013, > Mark > Plantz wrote: > > > I actually tried > to > view the > brainmask.mgz > file > with the > segmentation > file > [Freeview calls it > > 'registration > > file' I believe]. > > For some reason, > the > file will > load without > > segmentation, but when I > > attempt to add the > > registration > > file, I get an > > error > > message: > > "Failed to load > MRI > > ~/.../../../brainmask.mgz > > > Could this > > potentially be part of the > > problem? > > > Thanks > > > MP > > > > On Mon, Jul 29, > 2013 > at 10:57 AM, > Mark > > Plantz > > <markplantz2016(a)u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu> > > <mailto:markplantz2016@u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>>>> > > > wrote: > > > It looks > like > the values > vary from > > 20-120 > depending on > which > > region I run > the cursor > > over. > > However, aren't > > those the > > values > that > correspond to the > > brain.mgz regions? Is there > > another way to find the > > segmentation > > values? > > > > On Mon, Jul 29, > 2013 > at 10:37 AM, > Bruce > > Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > wrote: > > I mean the > > segmentation values that > give > you the "out > of bounds" > > message > > On Mon, 29 > Jul > 2013, Mark Plantz wrote: > > > Hi > > Bruce, > > Do > you > mean the > brainmask.mgz > > values? I'm not sure > what > the > segmentation #'s exactly > are. > > > > > Thanks! > > > MP > > > > On > Mon, > Jul 29, 2013 > at 10:17 > AM, > Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > wrote: > > > Hi > > ... > > [Message clipped] > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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functional ROI-based structural statistics?
by Yang, Daniel 06 Aug '13

06 Aug '13

Dear FreeSurfer Experts, Theoretically, if you have a set of functional ROIs, is it possible to derive the cortical thickness, white surface area, and gray matter volume of those functional ROIs in FreeSurfer? Many thanks!! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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