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choroid plexus
by Tracy Butler 08 Jun '11

08 Jun '11

Is there a good method to segment choroid plexus and calculate volume? I know it's an aseg label. Thanks, Tracy

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problem with annotation to label
by kwa1＠rice.edu 08 Jun '11

08 Jun '11

Hello, I am deriving a cortical region of interest label from FS from a series of normal controls. I have tried two different methods of obtaining these labels to see which is more consistent but neither are really acceptable. I am interested in the temporal pole label so first I did the normal mri_annotation2label for each subject but I don't know if it is a problem with segmentation or with vertex assignment, the TP labels can be wide and ranging and not consistent. Additionally, I tried taking the fsaverage subject and doing a label2label to map that TP label on to all the subjects but that was not good either. Does anyone know potentially what the problem can be and do you have any suggestions about how I can automatically derive a temporal pole label without having to get into manually drawing them (which would introduce a whole new array of issues with reliability). Thank you very much, Kareem

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Mri_glmfit-sim conceptual question
by John Richey 08 Jun '11

08 Jun '11

Dear freesurfer experts, I have a question about the conceptual use of mri_glmfit-sim. I wish to apply permutation based cluster-correction to my between-groups results (patients vs controls), and it is not clear to me which volume should be the input for this type of simulation. For example, the acceptable input for mri_glmfit-sim appears to be only the ".ces" map, which is not present in my between-groups directory, but only in my lower-level one-sample group means (osgm). This raises the question of whether to run the permutation algorithm 1) one time on the .ces map that results from the total sample OSGM (i.e. patients + controls), or 2) separately on OSGM for patients and then controls. Probably I am mistaken but neither seem to be conceptually correct, as I am mainly interested in the cwp for clusters emerging in the between-groups contrast. Any help would be greatly appreciated!

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pet partial volume correction
by corinna bauer 08 Jun '11

08 Jun '11

Hi all, I am wondering if partial volume is taken into account when calculating average uptake values of pet data. I know that aseg.stats takes partial volume into account and I am wondering if there is something similar in place for pet data? From what I gather, most people when using FreeSurfer correct for partial volume effects by regressing out cortical thickness, but no basis for this correction method has been provided. Any insight would be appreciated. n.b. to obtain the pet uptake values I used mri_segstats --seg mri/aparc+aseg.mgz --sum pet.segstats.dat --i $petanat --ctab rois.txt Thank you, Corinna

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FS5.1 OSX dyld: Library not loaded
by Michael O'Sullivan 08 Jun '11

08 Jun '11

I've encountered the same problem described below despite downloading the new version posted on 26th May. I downloaded freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg today from http://www.freesurfer.net/fswiki/Download I'm running Mac OS X version 10.6.7 (Intel) On attempting to test the installation as described in the instructions with tkmedit bert orig.mgz I get the message dyld: Library not loaded: /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib Referenced from: /Applications/IRIS/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap Is this the same library dependency issue, i.e. it's not fully fixed in the latest download at least not for my OS? I couldn't find any more recent posts but am new to the list, so apologies if I have. Thanks Mike Nick Schmansky Thu, 26 May 2011 05:59:24 -0700 Hyunwoo (and Mac users), A new build of v5.1 for the Mac (Leopard and Snow Leopard) has been posted. If you downloaded the one posted on May 24th, you will need to get this new one, as the one from May 24th depended on libgfortran, which is not installed natively. Sorry for any inconvenience. N. On Wed, 2011-05-25 at 14:57 -0400, Nick Schmansky wrote: > Hyunwoo (and Mac users), > > We're going to have to post a new build of v5.1 later today which fixes > this problem. In general, our goal is to have a Mac build that doesnt > require special libraries, like libgfortran, but both our build and test > machines had that lib for other reasons, so it slipped through the > cracks during testing. > > I'll post to the list when its ready. It will be identical in usage to > the current Mac 5.1, just without the libgfortran dynamic lib > dependency. > > Nick > > > On Wed, 2011-05-25 at 16:30 +0000, Hyunwoo Lee wrote: > > Dear FreeSurfer > > > > Hello, I am currently trying the following freesurfer version: > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwi…> > > and I noticed the following. > > During the first step ( recon-all -i invol1 -i invol2 -subjid > > your_subject_name ), the console displays the following messages: > > ------------------------------------------------------------------------------- > > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > INFO: SUBJECTS_DIR is ******* > > Actual FREESURFER_HOME /Applications/freesurfer > > Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 > > PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap

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Re: [Freesurfer] subcortical mask to MNI152 space
by Douglas N Greve 08 Jun '11

08 Jun '11

Hi Elisa, sorry about that. Yes, use the $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat instead. doug Elisa Golfinopoulos wrote: > Hi Doug, > > Thanks for responding to my inquiry. My version of Freesurfer (v.5) > does not contain > > mni152.mni305.cor.subfov2.dat > > in the average folder. I did notice that the most recent version of > freesurfer has the reg.2mm.mni152.dat > > in the same folder as the subcortical mask. > > Thanks so much for your help! > Take good care. > Elisa > > > On Tue, Jun 7, 2011 at 6:15 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Eventhough they are both in "MNI" space, there is still a > registration that has to be applied. Try something like this: > > > mri_vol2vol --mov > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz \ > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ > --reg $FREESURFER_HOME/average/mni152.mni305.cor.subfov2.dat \ > --o ./subcort.mask152.nii > > Elisa Golfinopoulos wrote: > > Hi, > > I would like to normalize the subcort.mask.mgz to MNI152 > space. I have attempted to use the command: > > mri_vol2vol --mov $FREESURFER_HOME/subjects/ > fsaverage/mri.2mm/subcort.mask.mgz > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz > --o ./subcort.mask152.nii > --reg $FREESURFER_HOME/average/mni152.register.dat > > but when I check the registration with the MNI152 template I > find that the 152 normalized subcortical mask does not align > with the template. The problem is somewhat resolved when I > specify a 180 degree rotation along the x axis (though there > still appears to be some translation error). However, I feel > uncomfortable using rotations/translations without > understanding why the registration is incorrect in the first > place. > > In fact, this problem is making me question whether a > transformation is really necessary since, technically, both > the mask and the target are in MNI space and the registration > of the original MNI 305 subcortical mask with the MNI152 > template looks more accurate than the 152 normalized mask. Any > help that you can offer would be greatly appreciated. > > Cheers, > Elisa > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> <tel:617.353.6181 > <tel:617.353.6181>> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 > <tel: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> > > > > 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. > > > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> > -- 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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Tracula Tutorial Dataset
by rspriti＠nmr.mgh.harvard.edu 08 Jun '11

08 Jun '11

Hi Freesurfers, An updated Tracula tutorial data is available for download through the following link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data And the tutorial to go with it can be accessed through the following link: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula Please let us know if you have any problems downloading the data or accessing the tutorial pages. Thanks, Priti

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MNI coordinates
by Elena Orekhova 08 Jun '11

08 Jun '11

Hi, I created a surface label from fsaverage and would like to know its coordinates in some commonly used space, such as e.g. talairach. The vertex 6111 coordinates look like this: 6111 35.2, 1.9, -27.0 0 In tksurfer the coordinates of the vertex 6111 are: Vertex RAS: (63.48 -12.29 0.35) Vertex Talairach: (62.85 -11.89 0.91) Apparently, the vertex RAS coordinates in the tksurfer do not correspond the vertex coordinates in the label. What are the label coordinates? How can I translate them to MNI/Talairach? I have seen the similar mail by Yolanda Vives, but no answer yet... Elena

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Thalamocortical Connectivity
by Kamal Abuhassan 08 Jun '11

08 Jun '11

Hi My PhD project focuses on developing a realistic thalamocortical model of Alzheimer's disease (AD). One of the major components of my project is to utilize DTI data from AD patients to build the macro-connectivity of the model. Currently, I'm working on FSL + FreeSurfer + CAMINO to process the DTI data. I'm sending this message to verify my approach in determining the regions of interest and to ask other critical questions. The approach A) Cortical Segmentation 1- First, I've segmented the T1-weighted image with recon-all command. 2- converted the cortical segmentation image (wmparc.mgz) into the Nifti format using mri_convert. B) Registration of Segmentation and Diffusion Weighted Image 1- The brain region was extracted from the b0 image using BET command 2- The output of the BET tool was used for the registration with the T1 image using FLIRT tool. 3- Obtain the inverse transformation matrix using convert_xfm in FSL 4- Apply the inverse matrix over the segmentation image with the 'Interpolation Method' as 'Nearest Neighbour' (using FLIRT). 5- Get the labels of Thalamus and cortical areas from usr/local/FreeSurfer/FreeSurferColorLUT.txt. (for cortical areas, I've considered cortical labels that started with 'wm-' but not 'ctx-'. Is that correct?) 6- Apply fslmath to pull out the appropriate ROI(s) 7- Apply Fiber Tracking tool to get fiber data. Questions: - Can you please advise if I'm doing right in outlining the ROI(s) ? - How can I differentiate between Thalamocortical and corticothalamic fibers ? - How can I get corticocortical fibers ? Is it right to get two cortical labels (source & destination) and find the pathways between them ? I will highly appreciate any advice/suggestions. Many Thanks Kamal.

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subcortical mask to MNI152 space
by Elisa Golfinopoulos 07 Jun '11

07 Jun '11

Hi, I would like to normalize the subcort.mask.mgz to MNI152 space. I have attempted to use the command: mri_vol2vol --mov $FREESURFER_HOME/subjects/ fsaverage/mri.2mm/subcort.mask.mgz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o ./subcort.mask152.nii --reg $FREESURFER_HOME/average/mni152.register.dat but when I check the registration with the MNI152 template I find that the 152 normalized subcortical mask does not align with the template. The problem is somewhat resolved when I specify a 180 degree rotation along the x axis (though there still appears to be some translation error). However, I feel uncomfortable using rotations/translations without understanding why the registration is incorrect in the first place. In fact, this problem is making me question whether a transformation is really necessary since, technically, both the mask and the target are in MNI space and the registration of the original MNI 305 subcortical mask with the MNI152 template looks more accurate than the 152 normalized mask. Any help that you can offer would be greatly appreciated. Cheers, Elisa -- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181

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