Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

hyperintense artifact causing problems for segmentation
by Sarah Whittle 20 Apr '11

20 Apr '11

Hi, I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a ring around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be quite labour intensive to manually remove the artefact, as it appears across most of the cortex. Has anyone seen this before and/or could offer advice as to the best way to proceed? Using the 3T flag in version 5 helps a little but far from perfect. Thanks, Sarah

3 5

Re: [Freesurfer] Pial surface error
by Allie Rosen 20 Apr '11

20 Apr '11

Hi, No, I'm not from the centre. I'm working on putting the files in Dropbox and sending you a link to them, because apparently I don't have ftp access. Allie On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu>wrote: > Are you from the center? If so you can just cd into /space/outgoing and > copy your file there. If not, you can follow the instructions in the box at > the top using a terminal. > > > On Tue, 19 Apr 2011, Allie Rosen wrote: > > Hi, >> >> I'm really sorry, but I don't understand those instructions. Do I login to >> the freesurfer website? Or do I login through a terminal somehow? Do I >> type >> the stuff in the boxes into the terminal? >> >> Thanks, >> Allie >> >> >> On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu >> >wrote: >> >> Hi Allie, >>> >>> You can compress the subject dir and upload it following the instructions >>> here >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>> >>> >>> >>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>> >>> Hi Khoa, >>> >>>> >>>> How do I upload subjects? >>>> >>>> Thanks, >>>> Allie >>>> >>>> >>>> >>>> On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu >>>> >>>>> wrote: >>>>> >>>> >>>> Hi Allie, >>>> >>>>> >>>>> Can you upload the subject? I'll take a look and see if I can figure >>>>> out >>>>> what's wrong. >>>>> >>>>> -Khoa >>>>> >>>>> >>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>> >>>>> Hi, >>>>> >>>>> >>>>>> This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. The >>>>>> part >>>>>> that wasn't included in the pial or white matter surfaces is still not >>>>>> included. The intensities in the white matter regions are no different >>>>>> than >>>>>> in white matter regions that were included in the white matter. Any >>>>>> other >>>>>> suggestions? >>>>>> >>>>>> Thanks, >>>>>> Allie >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen <rosen.allie(a)gmail.com> >>>>>> wrote: >>>>>> >>>>>> Hi Bruce, >>>>>> >>>>>> >>>>>>> I am running recon-all tonight using wm voxels that I manually added >>>>>>> (I >>>>>>> also edited brainmask.mgz to add missing grey matter). To me it >>>>>>> doesn't >>>>>>> really look like a case of the white matter not having a high enough >>>>>>> intensity. It simply looks like the whole lobe was ignored, >>>>>>> regardless >>>>>>> of >>>>>>> intensity. But I'll check tomorrow to see if the intensity is low. >>>>>>> >>>>>>> Thanks, >>>>>>> Allie >>>>>>> >>>>>>> >>>>>>> On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl < >>>>>>> fischl(a)nmr.mgh.harvard.edu>wrote: >>>>>>> >>>>>>> What is the intensity of the white matter in the regions you drew >>>>>>> in? >>>>>>> A >>>>>>> >>>>>>> couple of control points might help if it is less than 110 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Apr 18, 2011, at 12:36 PM, Allie Rosen <rosen.allie(a)gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Sita, >>>>>>>> >>>>>>>> Thanks for all the responses! I've actually had the same problem for >>>>>>>> multiple subjects. I'm using version 5.0.0. I'll try fixing the >>>>>>>> cerebellum >>>>>>>> as well. I've attached pictures of where I am adding wm voxels. They >>>>>>>> aren't >>>>>>>> really in the same places as in the online tutorials. Could you take >>>>>>>> a >>>>>>>> quick >>>>>>>> look to see if they're in the right place? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Allie >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori << >>>>>>>> sita(a)nmr.mgh.harvard.edu> >>>>>>>> sita(a)nmr.mgh.harvard.edu> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Hi Allie, >>>>>>>> >>>>>>>>> >>>>>>>>> pial surface which looks like this can only be corrected by >>>>>>>>> correcting >>>>>>>>> the wm.mgz. Also I would suggest to try and fix the cerebellum and >>>>>>>>> see >>>>>>>>> if it >>>>>>>>> corrects the surfaces as well. Since part of the cerebellum is >>>>>>>>> stripped >>>>>>>>> off, >>>>>>>>> it's probably affecting the segmentation as well but I could be >>>>>>>>> wrong. >>>>>>>>> what >>>>>>>>> version of freesurfer are you using. >>>>>>>>> >>>>>>>>> >>>>>>>>> Sita. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>> >>>>>>>>> Hi Sita, >>>>>>>>> >>>>>>>>> >>>>>>>>> Can I still add voxels to wm.mgz even though the points would be >>>>>>>>>> outside >>>>>>>>>> even the pial boundary? >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> Allie >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>>>>>>>>> < <sita(a)nmr.mgh.harvard.edu>sita(a)nmr.mgh.harvard.edu>wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi Allie, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> This probably needs white matter edits but it's hard to tell from >>>>>>>>>>> one >>>>>>>>>>> slice. Please refer to our white matter edits wiki and toplogical >>>>>>>>>>> defects >>>>>>>>>>> wiki and see if it helps in fixing the errors in your datasets. >>>>>>>>>>> Also >>>>>>>>>>> it >>>>>>>>>>> looks like part of the Cerebellum is stripped off. You might want >>>>>>>>>>> to >>>>>>>>>>> correct >>>>>>>>>>> that as well. >>>>>>>>>>> >>>>>>>>>>> < >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>> >>>>>>>>>>> < >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Sita. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Once processed, several of my subjects have had errors around >>>>>>>>>>> the >>>>>>>>>>> >>>>>>>>>>>> occipital >>>>>>>>>>>> lobe. Attached is an example. I've already tried editing >>>>>>>>>>>> brainmask.mgz >>>>>>>>>>>> and >>>>>>>>>>>> running recon-all, but as you can see, this didn't change the >>>>>>>>>>>> pial >>>>>>>>>>>> or >>>>>>>>>>>> wm >>>>>>>>>>>> borders. What can I do to fix this? >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> Allie Rosen, MSc Candidate >>>>>>>>>>>> Graduate Student, Department of Neurosurgery >>>>>>>>>>>> Toronto Western Hospital 14-327 >>>>>>>>>>>> 399 Bathurst St. >>>>>>>>>>>> University of Toronto >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 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. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> <2.png> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> <3.png> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>> >>

2 4

Compare left vs right hemisphere
by Alexandru Hanganu 20 Apr '11

20 Apr '11

Dear Doug, There´s a message in the list from Dec. 2008 about interhemispheric comparison, and you said there wasn't any good way to do this. Is there some new method included in FS 5.0 for right vs left hemisphere comparison ? Thanks. Sincerely, Alex. * *

1 0

mri_surfcluster threshold
by Elizabeth Gutierrez 19 Apr '11

19 Apr '11

Hi all, We're trying to create labels from a group level sig.mgh file. However, after the labels are created and an annotation file/color table is made, we try to view the sig.mgh file and the annotation file in tksurfer, but they don't extactly overlap, even though they are both configured to the same threshold (min-2 max-5). Most of the labels are fine, but the labels closest to the the higher end of the threshold end up being hollow, and only outline the sig.mgh clusters instead of being completely filled out. Does that make sense? Here is our command for mri_surfcluster: mri_surfcluster --in sig.mgh --hemi lh --subject fsaverage --thmin 2 --thmax 5 --sign pos --no-adjust --cwsig --o ./output_id --ocn ./cluster_number --olab ./grouplabel Thanks in advance! Elizabeth -- Elizabeth C. Gutierrez Graduate Student Department of Brain and Cognitive Sciences Massachusetts Institute of Technology

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Re: [Freesurfer] GLM problems
by Allie Rosen 19 Apr '11

19 Apr '11

Namely, I was following the directions from the following: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V On Tue, Apr 19, 2011 at 12:33 PM, Allie Rosen <rosen.allie(a)gmail.com> wrote: > Hi Doug, > > It worked with +1 -1 0. But I also have an agediff.mat file (0 0 +1 -1) > that I'd like to look at. Therefore I'd be looking at age differences and > also sex differences. Can I do this using DODS? I'm not sure if I'd be able > to do that with 3 regressors. > > So honestly I'm not even sure whether I should use DOSS or DODS. My groups > are male and female and I'm not sure if there are differences between them. > I thought that the first 2 regressors were male and female, and the 3rd and > 4th were age. Am I correct? > > Thanks, > Allie > > > > > On Tue, Apr 19, 2011 at 12:26 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> Hi Alli,e you are running it with DOSS which will create 4 regressors >> (MaleOffset, FemaleOff, AgeSlope). Your contrast has 4 columns. So change to >> DODS or change the number of column in your contrast. If you go with DODS, >> make sure to test for an interaction (ie, a contrast of 0 0 +1 -1). If you >> have substantial interaction, then testing the offsets is tricky. If you >> don't have an interaction, then change to DOSS and use (+1 -1 0). >> >> doug >> >> Allie Rosen wrote: >> >>> Update: ran on a different computer in the lab and progressed a little, >>> but got the following error: "dimension mismatch between X and contrast >>> sexdiff.mat X has 3 cols, C has 4 cols" >>> >>> I am not positive what X is, but here is my FSGD file (abbreviated): >>> >>> GroupDescriptorFile 1 >>> Class Male >>> Class Female >>> Variables Age >>> >>> Input C1 Female 27 >>> Input C2 Female 53 >>> Input C3 Male 22 >>> Input C4 Female 62 >>> Input C5 Male 27 >>> >>> And here is my contrast file: >>> >>> 1 -1 0 0 >>> >>> Any ideas? >>> >>> Thank you, >>> Allie >>> >>> >>> >>> >>> On Tue, Apr 19, 2011 at 11:51 AM, Allie Rosen <rosen.allie(a)gmail.com<mailto: >>> rosen.allie(a)gmail.com>> wrote: >>> >>> Hi All, >>> >>> I am running mri_glmfit and get the following error: >>> >>> mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss >>> --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> gdfReadHeader: reading fsgd2.txt >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> Continuous Variable Means (all subjects) >>> 0 Age 37.9483 >>> Class Means of each Continuous Variable >>> 1 Male 34.5417 >>> 2 Female 40.3529 >>> INFO: gd2mtx_method is doss >>> Reading source surface >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white >>> Number of vertices 163842 >>> Number of faces 327680 >>> Total area 65416.648438 >>> AvgVtxArea 0.399267 >>> AvgVtxDist 0.721953 >>> StdVtxDist 0.195470 >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ >>> cwd /media/AMMONIS/fsSubjects/AR_normals >>> cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt >>> doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> sysname Linux >>> hostname Caduceus >>> machine x86_64 >>> user arosen >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz >>> logyflag 0 >>> usedti 0 >>> FSGD fsgd2.txt >>> labelmask >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label >>> maskinv 0 >>> glmdir lh.insula.thickness.6.glmdir >>> IllCondOK 0 >>> DoFFx 0 >>> Creating output directory lh.insula.thickness.6.glmdir >>> Segmentation fault >>> >>> >>> The directory IS created, but contains only "mri_glmfit.log". Here >>> are the contents: >>> >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ >>> cwd /media/AMMONIS/fsSubjects/AR_normals >>> cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt >>> doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> sysname Linux >>> hostname Caduceus >>> machine x86_64 >>> user arosen >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz >>> logyflag 0 >>> usedti 0 >>> FSGD fsgd2.txt >>> labelmask >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label >>> maskinv 0 >>> glmdir lh.insula.thickness.6.glmdir >>> IllCondOK 0 >>> DoFFx 0 >>> >>> If this all sounds familiar, I realize that I've submitted this >>> problem back in January and haven't managed to work it out. Any >>> help would be appreciated! >>> >>> Thank you, >>> Allie Rosen, MSc Candidate >>> Graduate Student, Department of Neurosurgery >>> Toronto Western Hospital 14-327 >>> 399 Bathurst St. >>> University of Toronto >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> >

2 1

GLM problems
by Allie Rosen 19 Apr '11

19 Apr '11

Hi All, I am running mri_glmfit and get the following error: mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat gdfReadHeader: reading fsgd2.txt INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 37.9483 Class Means of each Continuous Variable 1 Male 34.5417 2 Female 40.3529 INFO: gd2mtx_method is doss Reading source surface /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 Creating output directory lh.insula.thickness.6.glmdir Segmentation fault The directory IS created, but contains only "mri_glmfit.log". Here are the contents: $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 If this all sounds familiar, I realize that I've submitted this problem back in January and haven't managed to work it out. Any help would be appreciated! Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

2 2

Re: [Freesurfer] Pial surface error
by Allie Rosen 19 Apr '11

19 Apr '11

Hi Sita, Thanks for all the responses! I've actually had the same problem for multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. I've attached pictures of where I am adding wm voxels. They aren't really in the same places as in the online tutorials. Could you take a quick look to see if they're in the right place? Thanks, Allie On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <sita(a)nmr.mgh.harvard.edu>wrote: > > Hi Allie, > > pial surface which looks like this can only be corrected by correcting the > wm.mgz. Also I would suggest to try and fix the cerebellum and see if it > corrects the surfaces as well. Since part of the cerebellum is stripped off, > it's probably affecting the segmentation as well but I could be wrong. what > version of freesurfer are you using. > > > Sita. > > > > On Mon, 18 Apr 2011, Allie Rosen wrote: > > Hi Sita, >> >> Can I still add voxels to wm.mgz even though the points would be outside >> even the pial boundary? >> >> Thanks >> Allie >> >> >> >> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >> <sita(a)nmr.mgh.harvard.edu>wrote: >> >> >>> Hi Allie, >>> >>> This probably needs white matter edits but it's hard to tell from one >>> slice. Please refer to our white matter edits wiki and toplogical defects >>> wiki and see if it helps in fixing the errors in your datasets. Also it >>> looks like part of the Cerebellum is stripped off. You might want to >>> correct >>> that as well. >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>> >>> >>> Sita. >>> >>> >>> >>> >>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>> >>>> >>>> Once processed, several of my subjects have had errors around the >>>> occipital >>>> lobe. Attached is an example. I've already tried editing brainmask.mgz >>>> and >>>> running recon-all, but as you can see, this didn't change the pial or wm >>>> borders. What can I do to fix this? >>>> >>>> Thank you, >>>> Allie Rosen, MSc Candidate >>>> Graduate Student, Department of Neurosurgery >>>> Toronto Western Hospital 14-327 >>>> 399 Bathurst St. >>>> University of Toronto >>>> >>>> >>>> >>> 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. >>> >>> >>> >>

3 5

roi from icbm152 to fsaverage inflated surface
by Boris Bernhardt 19 Apr '11

19 Apr '11

Dear Freesurfers, Using FreeSurfer 4.5.0, I am trying to map a binary *.nii roi-mask (defined in ${LABEL}) that has been outlined on the icbm-152 template in mni space to the inflated surface model of fsaverage. The approach below gives me a solution that looks very trustworthy, however, I'd like to verify with the experts whether it is 100% accurate. These are the commands I am using: # to map the label to the fsaverage target mri_label2vol --seg ${LABEL} --temp fsaverage/mri/orig.mgz --reg ${FREESURFER_HOME}/average/mni152.register.dat --invertmtrx -fillthresh 0.5 --o ${LABEL%.nii}_fsa.nii # to intersect it with the wm surface, and then map it to the sphere (note that identity.dat has been generate prior to running the command). mri_vol2surf --src ${LABEL%.nii}_fsa.nii --reg identity.dat --hemi lh --surf white --interp nearest --surfreg sphere.reg --icoorder 7 --out ${LABEL%.nii}_fsasurf_lh.mgh # to convert the mgh to ascii mris_convert -c ${LABEL%.nii}_fsasurf_lh.mgh fsaverage/surf/lh.white {LABEL%.nii}_fsasurf_lh.asc Many thanks, Boris

1 0

Retinotopy-polar angle
by Michelle Umali 19 Apr '11

19 Apr '11

Dear Freesurfers, I'm having issues trying to display the polar angle data using the color wheel. Unfortunately, I can't resizing the Configure Overlay Display window. No matter what I try, I can't actually see the Apply button. Any suggestions? Also, is there a quickie guide on defining the boundaries of visual areas? Thanks. Michelle

2 2

Fedora 14
by roger.jou＠yale.edu 18 Apr '11

18 Apr '11

Hi all, Quick question: will the latest Linux 32-bit install work with Fedora 14? Please let me know if there are known issues. Thanks, Roger

2 1

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