Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

groups stats doubts
by Gabriel Go.Es. 15 Sep '10

15 Sep '10

I'm going to run some analyses and have some doubts with respect to the general approach that I should follow. We want to evaluate differences in cortical thickness in three different groups. Shoud I perform an ANOVA (to know if there is a group effect) followed by pairwise comparisons (to localize the difference)? If so, what should I do if results from the ANOVA and pairwise comparisons are localized in different regions? Shoud I restrict the pairwise contrasts to regions where ANOVA revealed significant differences? Many thanks in advance. Best Regards Gabriel

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Re: [Freesurfer] How to access host files in the freesurfer virtualBox.
by Darren Gitelman 14 Sep '10

14 Sep '10

Nevermind. I was able to install the additions, and then with disabling 3D acceleration freesurfer works. Darren

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How to access host files in the freesurfer virtualBox.
by Darren Gitelman 14 Sep '10

14 Sep '10

Hi Does anyone know how to access the host's drive when using VirtualBox? The problem is (I don't think) that one can install the VirtualBox Guest Additions as it messes up the graphics for freesurfer (at least it did for me). However the VirtualBox guest additions contain the kernel extensions to mount the host's drives. Is there any way to just install access to the virtual drives or to access the drives in some other way? I am running Freesurfer VirtualBox on a windows 7 system. Thanks, Darren

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Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45
by Darren Gitelman 14 Sep '10

14 Sep '10

I have figured out how to increase the size of the Freesurfer Virtualbox disk. This turned out to be non-trivial and was greatly facilitated by the CloneVDI tool. I tried a number of methods before using this tool but they did not result in a bootable virtual disk for reasons that remain unclear to me. Those methods include creating a new larger virtual disk, then using gparted to copy the old disk contents to the new disk contents and then expanding the disk to fill the new larger space. I also tried using the unix dd utility to copy the old to new disk and using the VBoxManage command line program to try to clone the disk. The instructions below require some familiarity with using unix tools such as gparted to setup the disk. If you have no experience with this find someone who does. I should probably add that your virtual box should be shutdown before you do any of this and you should have made a backup copy in case you select the wrong virtual disk in this process and mess it up. (The usual disclaimer applies- i.e., if you mess up your freesurfer virtual disk with all your data, and don't have a backup, it's your problem.) The CloneVDI tool, (get it here: http://forums.virtualbox.org/viewtopic.php?f=6&t=22422) works like a charm. Start the tool and you will see a GUI for cloning your freesurfer vdi disk. You just select your current freesurfer vdi file as the source, and then a new destination vdi file. I generated a new UUID for the new disk and increased the virtual drive size to 25 GB (but you can choose whatever size you want). Then click proceed. Once the new disk is generated you will need to fix it up a bit with gparted. The overview is that when you examine the disk in gparted you will notice that the old filesystem occupies only a portion of the disk (the first partition). This is followed by an extended partition that contains a linux swap partition. In order to expand the size of the freesurfer installation you will need to delete the linux swap and the extended partition, enlarge the primary partition and then recreate the extended partition and the linux swap. The steps are as follows: Download the gparted-live iso ( http://sourceforge.net/projects/gparted/files/gparted-live-stable/) Start virtualbox, open the virtual media manager and add the gparted-live iso under CD/DVD images. Also add the new cloned hard disk. Now open the virtual box settings. Under storage you will need to add the new virtual hard disk and change it to be the primary master. (You will have to change the old freesurfer virtual disk to be the secondary slave and then you can select the new disk as the primary master. Also make sure the gparted-live disk (iso) is selected as the CD/DVD device. Now boot the virtualbox and immediately press F12 which allows you to select the boot device. Choose the gparted-live CD. Once gparted starts it should recognize your visual disks and show them in the GUI. Make sure you have selected your new visual disk and NOT the old one. If you have properly designated the new virtual disk as the primary master it should be identified as /dev/sda. You should notice that there is a primary partition (/dev/sda1) which is your freesurfer installation. There will also be an extended partition (/dev/sda2) that contains the swap partition (/dev/sda5). Delete the swap partition and then the extended partition. Now expand the primary partition consistent with your new disk size BUT remember to leave room for the swap partition. (You must have a swap partition on linux or the installation definitely won't work properly.) The old swap was 400 MB but if you increase the RAM on your virtual disk you may want the swap to be 2 GB. So for a 25 GB disk your primary partition will be about 23 GB and swap will be 2 GB. After expanding the primary partition, recreate the extended partition as /dev/sda2 and then within that recreate the linux-swap partition- it will be /dev/sda5. Apply the changes, and then shutdown gparted. Now unmount the gparted-disk and you can also unmount your old freesurfer installation. Reboot and voila (if everything worked correctly) you will have the your freesurfer installation and oodles (or GB) of additional disk space. Happy freesurfing, Darren P.S: I don't monitor the freesurfer list so email both the list and me (d DOT gitelman AT gmail DOT com) if there are questions about this. I will try to answer, but no promises as to when.

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problem with mri_fill
by SM Chita 14 Sep '10

14 Sep '10

Hello gentle readers and experts of FreeSurfer, I am using the FS software package to calculate the gyrification index for premature baby brain. Of course in order to get to this step I do need to run the previous autorecon steps to obtain the pial surface. So far I've run the first sequence for one of my test subjects, recon-all -autorecon1, and encountered no errors. For the second step autorecon2 I have decided to run every subsequent step, firstly, because if I understand correctly from the wiki-webpage the flag -noaseg is necessary if the subjects cannot use an aseg, like baby brain. Secondly, due to the poor T1,T2 intensity contrast in my baby-scans the FS default segmentation step was not performed correctly (large portions of white matter were not counted). So I include my own segmented white matter volume. To include my WM volume I have used "mri_convert -c" to convert analyze data into .mgz format. The steps from the second sequence that I ran without getting any errors are: "-gcareg", "-canorm", "-careg", "-careginv", "- rmneck", "-skull-lta", "-normalization2 -noaseg", "-maskbfs" . At the step "-fill -noaseg" the errors are: min_slice = -1, min_area = 65536 mri_fill: could not find corpus callosum find_cutting_plane:seed point not in structure! Searching neighborhood... recon-all -s blob2test exited with ERRORS at Tue Sep 14 13:18:14 CEST 2010 After this error I used the command: "recon-all -fill -cc-crs -pons-crs -lh-crs -rh-crs -noaseg -s blob2test" and got a bus error: /Applications/freesurfer/subjects/blob2test/mri \n mri_fill -a ../scripts/ponscc.cut.log -Cv -pons-crs -lh-crs -rh-crs -xform transforms/talairach.lta wm.mgz filled.mgz \n logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position ( 0, 0, 0) as corpus callosum seed point INFO: Using transforms/talairach.lta and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 2.694 0.124 -0.276 -194.089; -0.311 2.259 -0.788 -3.124; 0.090 0.794 2.183 -266.051; 0.000 0.000 0.000 1.000; Bus error recon-all -s blob2test exited with ERRORS at Tue Sep 14 13:20:58 CEST 2010 My suspicion is that the way I have converted my WM volume is not correct and since the -fill uses the wm.mgz I do get error on this step. However I also tried to "align" my wm.mgz with brain.mgz using: "mri_convert mywm.mgz mynewwm.mgz --like brain.mgz". The "--apply_transform" option is not really clear to me and I do not get any good results if I apply that to mywhitematter.mgz. I also used tkregister2 to align the two volumes: my white matter with brain.mgz for example. But the wm.mgz file I've saved after registration to brain.mgz it could not be opened in tkmedit anymore so I decided not to use it as wm.mgz further. I do want to use my white matter segmentation and continue with the steps in order to calculate with FS a pial surface, inflated surface, gyrification index, etc. for both hemispheres. I am also aware of the fact that using an adult atlas for baby scans is not correct so this might be also causing errors. One next step would probable be to make a baby brain atlas and include that instead of the */average/*.gca files. What do you suggest as first starting point in solving the errors? Thanks a million for your answer !! Best regards, Sabina

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Re: [Freesurfer] Re-run FreeSurfer with V.5.0
by Douglas N Greve 14 Sep '10

14 Sep '10

Hi Jordi, The edits will automatically be incorporated when you run version 5. Assuming that the edits you made were correct (eg, control points are in white matter), then the edits that you made in previous versions will be valid for version 5 (though you might not have had to have made those edits if you had run v5 from scratch). doug Jordi Delgado wrote: > Hi, > > I have a question related to this thread. If we have made manual > modifications using tkmedit (control points, pial, wm) with 4.3.1 > version and now we would like to run these subjects with version 5, is > it posible? What implications we will have to take into account, or > maybe for each new freesurfer version we have to start from scratch? > > I assume that the transfer of the manual modifications from an old > version to the 5 version, doesn't make sense because for every > processing with a new version the result will not be the same and we > have to modify the images according to the 5 version results. > > Thank you, > > 2010/9/13 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > yes (but make sure to make backups). > > doug > > Gina Caetano wrote: > > Hello, > > > > Version 4.2.0 was used to start processing data for a 3-years > project. > > We are still acquiring data for the project, and would like to start > > using version 5.0. > > > > For some of the subjects already processed, manual talairach > alignment > > was performed with tkregister2, and as I understood when recon-all > > -autorecon1 is run it will not overwrite this alignment. Former > > processing also contains manual edits to the brainmsak.mgz, > wm.mgz as > > well as control points, and as I understood when re-running > autorecon2 > > the manual edits will be saved by default. > > > > Thus, I am thinking to re-run all the recon-all steps when changing > > from v4.2 to v.5.0. Would you advise it? > > > > Thank you all in advance, > > > > > > Gina > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Jordi Delgado Mengual > PIC (Port d'Informació Científica) > Campus UAB, Edifici D > E-08193 Bellaterra, Barcelona > Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 > http://www.pic.es > Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- 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

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Surface file coordinate system
by John Schulman 14 Sep '10

14 Sep '10

I'm looking at an ascii version of a surface file generated by freesurfer. #!ascii version of patch ./lh.orig. The 1st index is not a vertex number 150463 299577 1 vno=0 27.392525 -134.276505 -66.754089 2 vno=1 27.100813 -134.257095 -66.985382 3 vno=2 26.631136 -134.229446 -67.306076 4 vno=3 29.255196 -134.120728 -65.788467 etc. In what coordinate system are these vertices? I want to convert to ijk index from the anatomical volume used to make the surface.

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Re: [Freesurfer] problem of mri_vol2surf
by Douglas N Greve 13 Sep '10

13 Sep '10

The 27307 x 6 was originally done to be able to store data in nifti and analyze formats. They can be reshaped into a single vector of length 163842. When you load it into tksurfer, do you set the threshold to something very close to 0 to see if your values are just too small? Is everything 0 in matlab? Did you check the registration? doug Jing Ming wrote: > Hi Doug: > > what I meant here is when we load output file on fsaverage surface, > we can see nothing. And I have a question, why the mri_vol2surf need > to reshape the whole vertex vector into 27307 x 6 dimention? > > Reshaping 6 (nvertices = 163842) > > > Writing to ./sig-rh.mgh > > > Dim: 27307 1 6 > > I have been able to load this mgh file into matlab, and should I > just need to concatenate the six row of data to reconstruct a complete > vector corresponding to the suface template? > > Thanks much for your help! > > Jing > > > > > > > Date: Mon, 13 Sep 2010 13:19:40 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: mj_coming(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] problem of mri_vol2surf > > > > what do you mean that you were not able to overlay it on the surface? > > What is actually going wrong? It looks like mri_vol2surf complete > > succesffully. > > > > doug > > > > Jing Ming wrote: > > > Hi surfers: > > > > > > I was trying to convert a volume dataset from PET to fs surface > > > template. The command I used is the following: > > > > > > mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o > > > ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico > > > --icoorder 7 > > > > > > The output file here is .mgh format. I also tried paint format. > > > However, I was not able overlay the surface file (.mgh or .w) using > > > freesufer. Is there anythign wrong with the command line? > > > > > > Here is the the output log: > > > ************************************************** > > > IcoOrder = 7, nIcoVtxs = 163842 > > > srcvol = pet2t1.mgz > > > srcreg = register.dat > > > srcregold = 0 > > > srcwarp unspecified > > > surf = white > > > hemi = rh > > > trgsubject = ico > > > surfreg = sphere.reg > > > interp = nearest > > > float2int = round > > > GetProjMax = 0 > > > INFO: float2int code = 0 > > > Done loading volume > > > Reading surface > /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white > > > Done reading source surface > > > Mapping Source Volume onto Source Subject Surface > > > 1 0 0 0 > > > vol2surf_linear: nhits = 152282/152282 > > > Done mapping volume to surface > > > Number of source voxels hit = 94326 > > > Reading source surface registration > > > > /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg > > > Done loading source registration surface > > > Reading icosahedron, order = 7, radius = 100 > > > Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri > > > Done loading target registration surface > > > Mapping Surfaces (127_S_1210X1a_63646 -> ico) > > > surf2surf_nnfr: building source hash (res=16). > > > Surf2Surf: Forward Loop (163842) > > > > > > surf2surf_nnfr: building target hash (res=16). > > > Surf2Surf: Reverse Loop (152282) > > > Reverse Loop had 34160 hits > > > Surf2Surf: Dividing by number of hits (163842) > > > INFO: nSrcLost = 0 > > > Done mapping surfaces > > > nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits > = 2.2761 > > > nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 > > > Reshaping 6 (nvertices = 163842) > > > Writing to ./sig-rh.mgh > > > Dim: 27307 1 6 > > > ************************************************** > > > > > > Thanks > > > Jing Ming > > > Northwestern University > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > -- 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

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Re: [Freesurfer] Re-run FreeSurfer with V.5.0
by Gina Caetano 13 Sep '10

13 Sep '10

Hello, Version 4.2.0 was used to start processing data for a 3-years project. We are still acquiring data for the project, and would like to start using version 5.0. For some of the subjects already processed, manual talairach alignment was performed with tkregister2, and as I understood when recon-all -autorecon1 is run it will not overwrite this alignment. Former processing also contains manual edits to the brainmsak.mgz, wm.mgz as well as control points, and as I understood when re-running autorecon2 the manual edits will be saved by default. Thus, I am thinking to re-run all the recon-all steps when changing from v4.2 to v.5.0. Would you advise it? Thank you all in advance, Gina

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problem of mri_vol2surf
by Jing Ming 13 Sep '10

13 Sep '10

Hi surfers: I was trying to convert a volume dataset from PET to fs surface template. The command I used is the following: mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico --icoorder 7 The output file here is .mgh format. I also tried paint format. However, I was not able overlay the surface file (.mgh or .w) using freesufer. Is there anythign wrong with the command line? Here is the the output log: ************************************************** IcoOrder = 7, nIcoVtxs = 163842 srcvol = pet2t1.mgz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ico surfreg = sphere.reg interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 152282/152282 Done mapping volume to surface Number of source voxels hit = 94326 Reading source surface registration /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg Done loading source registration surface Reading icosahedron, order = 7, radius = 100 Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri Done loading target registration surface Mapping Surfaces (127_S_1210X1a_63646 -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (152282) Reverse Loop had 34160 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits = 2.2761 nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 Reshaping 6 (nvertices = 163842) Writing to ./sig-rh.mgh Dim: 27307 1 6 ************************************************** Thanks Jing Ming Northwestern University

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