Freesurfer

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19 participants
30132 discussions

Basal Ganglia Components
by Dhinakaran Chinappen 17 Nov '10

17 Nov '10

Dear all, Hope your research is going smoothly. My question refers to the basal ganglai components. I previously shot an email which Prof. Fischl was kind enough to reply to: the basal ganglia is not computed as a structure of its own in FreeSurfer. These are the structures of the basal ganglia one can gather: (1) striatum (Caudate and putament) (2) Ventral Striatum - (a) nucleus accumbens (b) most ventral aspects of caudate and putament (3) Celobus pallidus (internal and external sectors) (4) Substancia Nigra (5) Subthalamic nucleus Here are my questions: => Structures (1), (2), (3) and (4) can be found... however, am having trouble locating the segmentation label number for the subthalamic nucleus. => The output for (4) is not reported in asegstats2table (while other structures are). Any other suggestions to extract the volume out? Thanks, Dhinakaran.

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make_average_subject
by tulu＠ms36.hinet.net 17 Nov '10

17 Nov '10

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label statistics
by Sasa Kivisaari 17 Nov '10

17 Nov '10

Hi all, Is there a way of ouputting all the thickness values (vertex by vertex) within a specified label? I would like to get some more information out of my labels than is provided by mris_anatomical_stats. All the best, Sasa

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3D view in freeview
by Marco Loggia 17 Nov '10

17 Nov '10

Dear all, I am trying to use the 3D view in freeview to prepare some figures, and would like to be able to rotate the volume along one axis only (e.g., yaw). Is there a way to constrain the rotation with the mouse, and/or to enter the numerical value of parameters such as azimuth and elevation? Thanks, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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export in stl format
by Miguel Burgaleta 17 Nov '10

17 Nov '10

Hi FreeSurfers, I am converting the pial surface (?h.pial) into STL format and importing it into Blender as described in http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel. However, I would like to end up with a render of the whole brain (i.e. including both hemispheres, cerebellum, brainstem, etc). Is there any easy way to do this from the FreeSurfer's output? Thanks! Miguel

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Re: [Freesurfer] Mean lGI value extraction
by Marie Schaer 17 Nov '10

17 Nov '10

Sorry Prapti, I was confused, the exact commands are: mris_anatomical_stats -a aparc.annot -t pial_lgi -f #SUBJ/stats/ lh.aparc_lgi.stats #SUBJ lh and then aparcstats2table --subjects #SUBJ1 #SUBJ2 ... --hemi lh --meas thickness --parc aparc_lgi --t YOUR_OUTPUT_TABLE Hope it will work, Marie On 17 nov. 10, at 02:44, Prapti Gautam wrote: > > > Hi Marie, > > I've done what was suggested but I've encountered a problem. I will > recount my steps: > > I used mri_anatomical_stats to create a file called lh.lgi.stats in > the label directory of subjects. I've double checked to see that the > file indeed contains lgi values and not thickness values (they are > different values from a separately tabulated files for thickness) > > next I'm trying to pass this file as the input to the > aparcstats2table with the command you specified. The syntax I ran is: > > > aparcstats2table --hemi lh --subject test --measure thickness -- > tablefile test/label/lh.lgi.stats -t lh.lgi.table > > My output is now saved in the file lh.lgi.table, but it contains > thickness values instead of lgi values from the tablefile. Can you > please tell me what I am missing here? > > thank you, > > Prapti > > -----Original Message----- > From: Marie Schaer [mailto:Marie.Schaer@unige.ch] > Sent: Wed 11/17/2010 12:39 AM > To: Prapti Gautam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mean lGI value extraction > > Hi Prapti, > > Normally you can use aparcstats2table exactly as you would do with > thickness, given that the column corresponding to thickness values in > the tablefile that you produced with your mris_anatomical_stats are > indeed lgi values (i.e. you used mris_anatomical_stats -t pial_lgi -f > lh.lgi.stats, which allows you to use: aparcstats2table -- > subjects ...... --hemi ?h --measure thickness --tablefile ? > h.lgi.stats). > > Let me know if you encounter any problem, > > Marie > > > On 16 nov. 10, at 04:28, Prapti Gautam wrote: > >> dear all, >> >> I am trying to extract the mean values of lgi from the cortex from a >> group of subjects. I found the following command useful in >> extracting for one subject: >> >> mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c >> lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh >> >> However, I have a lot of subjects I wish to extract this for and I >> was wondering if there is a command that will extract these values >> similar to the aparcstats2table command (where all the subjects and >> the mean values for each parcellation is in one output file) >> >> thanks, >> >> Prapti >> >> _______________________________________________ >> 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. >> > > > >

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absolute differences using paired diff?
by Mayuresh 16 Nov '10

16 Nov '10

Hi Doug, Nick and other freesurfer users, I have two groups and each group has a matched pair of subjects. I am keen on identifying cortical areas where the difference between the matched pair in group1 is greater than that in group2. How can I do this in freesurfer? >From the email archive it seems to me that -paired-diff option with mris_preproc should do the trick, however as I understand this will create difference maps such that subject1-matchedsubject2. For my purpose I would be needing the absolute difference between the pairs. How can I acheive this? Thanks for any pointers, Mayuresh

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GPU CUDA on Snow Leopard
by Pedro Paulo de Magalhães Oliveira Junior 16 Nov '10

16 Nov '10

Is there a plan to release the FreeSurfer CUDA Binaries for Snow Leopard? Thanks PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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Cortical thickness of a Volume-defined ROI: Reshaping dimensions
by Righart, Ruthger Dr. 16 Nov '10

16 Nov '10

Dear Freesurfers, I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my ROI went well! After that I would like to get thickness data using mri_segstats (step 5). However, Freesurfer indicates that the dimensions of my segmentation image (23406 x 1 x 7) are different from the dimensions of my input image (27307 x 1 x 6), and using mri_info suggests that sth seems to have gone wrong in step 4. I have searched in the Freesurfer archives and I understood that 23406 x 1 x 7 are the correct dimension values and followed the advise to use --reshape in the fourth step. This does however not change the dimensions (it still indicates in the Freesurfer output: Reshaping 6 (nvertices = 163842) which I guess should be Reshaping 7). Any suggestions to solve this problem of different dimensions are very much appreciated! Best Regards, Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de

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Mean lGI value extraction
by Prapti Gautam 16 Nov '10

16 Nov '10

dear all, I am trying to extract the mean values of lgi from the cortex from a group of subjects. I found the following command useful in extracting for one subject: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh However, I have a lot of subjects I wish to extract this for and I was wondering if there is a command that will extract these values similar to the aparcstats2table command (where all the subjects and the mean values for each parcellation is in one output file) thanks, Prapti

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