[Freesurfer] Subdividing the automated cortical parcellation
Dear experts Using cortical thickness analysis with Freesurfer I would like to compute small world network indices in a special population. The automated parcellating system is resulting in 66 cortical areas. For our purpose, I would like to subdivide these areas into smaller ones. (A similar methodology was applied by Hagmann et al., PLoS Biol 6: 14791493, 2008.) Does a finer parcellation scheme become part of future Freesurfer releases? Or have someone some experience in such a procedure? Any information would be much appreciated. Kind regards Diana Wotruba ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Subdividing the automated cortical parcellation/normalization
This worked perfectly well, thanks a lot for your quick answer! I would appreciate to get some input for the following issue. I run the mris_divide_parcellation on the fsaverage brain getting about 1000 parcellations: mris_divide_parcellation fsaverage_fineparc rh aparc.a2005s_150.annot 150 rh_annot_100 Now I would like to spatially register these labels onto each subject's brain, in order to bring these parcellations into a common standard space so that we can compare the parcellations across subjects. I there a manual or a tool for such a procedure? Thanks in advance Regards Diana On Fri, 16 Jan 2009 12:48:44 -0500 (EST) Bruce Fischl wrote: Hi Diana, you can try mris_divide_parcellation, which I think we distribute. If you don't have it tell us your os/hardware and we'll send you a version. cheers, Bruce On Fri, 16 Jan 2009, Diana Wotruba wrote: Dear experts Using cortical thickness analysis with Freesurfer I would like to compute small world network indices in a special population. The automated parcellating system is resulting in 66 cortical areas. For our purpose, I would like to subdivide these areas into smaller ones. (A similar methodology was applied by Hagmann et al., PLoS Biol 6: 14791493, 2008.) Does a finer parcellation scheme become part of future Freesurfer releases? Or have someone some experience in such a procedure? Any information would be much appreciated. Kind regards Diana Wotruba ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_divide_parcellation
Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) into about 1000 smaller parcellations, using mri_divide_parcellation. What would be the easiest way to get the cortical thickness in these areas for each subject? Is it reasonable to copy the new .annot file from fsaverage into each subjects label folder ensuing mris_anatomical_stats? Any help would be appreciated Regards Diana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aparcstats2table bug
Dear experts If some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them. According to the freesurfers website, this bug will be fixed in the next release. Is it already known when this can be expected? Thanks in advance Diana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparcstats2table new version (-parc)
Dear Pratap The file is called ?h.aparc.a2005s_300.stats as you suggested. The commands I used are the following: mris_divide_parcellation fsaverage_fineparc ?h aparc.a2005s.annot 300 ?h.aparc.a2005s_300.annot mri_surf2surf --srcsubject fsaverage_fineparc --sval-annot aparc.a2005s_300.annot --trgsubject 001--tval aparc.a2005s_300.annot --hemi ?h mris_anatomical_stats -a aparc.a2005s_300.annot -t ?h.thickness -b -f 001/stats/?h.aparc.a2005s_300.stats 001 ?h aparcstats2table --subjects 001 002 003 --hemi ?h --parc aparc.a2005s_300 --meas thickness -t ?h_aparc.a2005s_300_stat.txt Thanks for your help Diana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aparcstats2table new version (-parc)
Hi Krish Thanks again for your quick help! I tried out the new version, it seams to work fine. Nevertheless, I created a new parcellation with mris_anatomical_stats getting a .stat file I called aparc.a2005s_300. Only now I get the following error message (Which was not the case in the former version): aparcstats2table: error: option --parc: invalid choice: 'aparc.a2005s_300' (choose from 'aparc', 'aparc.a2005s') How can I force the -parc option to read my own parcellations? Diana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_anatomical_stats segmentation fault
Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) with an area threshold of 100mm2. Now I would like to get a stats file, using the following command: mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 001/stats/?h.aparc.a2005s_100.stats 001 ?h I am getting the following error message: "Segmentation fault" (after 1374 entries are read) The same command works just fine with a parcellated .annot file I generated with a lower threshold (p.e. 150mm2). Any help would be appreciated Regards Diana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] microparcellation
Dear Nick Is it possible to refer the "faces" I got with the command below to the labels from an annotation file? [Macintosh-10:subjects/fsaverage_fineparc_uniformareas/surf] diana% mris_make_face_parcellation rh.inflated /Applications/freesurfer/lib/bem/ic4.tri rh.ic4.annot I would like to run the following commands from the .annot file I generated with the mris_make_face_parcellation in order to get a txt-file with, for example, the cortical thickness information in each face: mri_surf2surf mris_anatomical_stats aparcstats2table With this procedure I would lose the precise site of a face and its associated anatomical label. Thank you very much for your help! Diana On Mon, 02 Mar 2009 14:44:54 -0500 Nick Schmansky wrote: Jose, mris_make_face_parcellation is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc for three of the supported platforms. Nick On Mon, 2009-03-02 at 13:23 -0500, Bruce Fischl wrote: Hi Jose, this looks pretty much correct. We have another utility, called mris_make_face_parcellation that can be used to generate parcellation units of mostly uniform area over the surface of the cortex. If you tell us your hardware/software environment we can give you a beta. cheers, Bruce On Mon, 2 Mar 2009, Jose Luis Cantero Lorente wrote: > Dear Freesurfers, > > We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code? > > Thank you very much in advance. > > Best, > Jose > > --- > Jose Luis Cantero, Ph.D. > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cellular Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Sevilla > - Spain - > > Phone: +34 954 977433 > Fax: +34 954 349151 > Email: jlcan...@upo.es > http://www.upo.es/neuroaging/es/ > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_make_face_parcellation
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations. In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot. In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations. All suggestions are appreciated. Thanks in advance Best regards Diana ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_make_face_parcellation
Hi Bruce Thank you for the quick answer. We already considered using mris_divide_parcellation. Unfortunately the result is a strip shaped parcellation scheme, which is not suitable for our aim. Therefore we would rather use mris_make_face_parcellation. Is there no other way to get the MNI Coordinates of these vertices and the label corresponding to them? Thanks very much for your help! Kind regards Diana Am 12.04.2010 um 00:31 schrieb Bruce Fischl: > Hi Diana, > > the parcels from mris_make_face_parcellation are uniform, not > localized > to gyral/sulcal labels. If that is important try using > mris_divide_parcellation instead. > > cheers > Bruce > > > On Sun, 11 Apr 2010, Diana > Wotruba wrote: > >> Dear FS experts >> We used mris_make_face_parcellation to get a finer parcellation of >> the >> cortical surface. The labels of the resulting parcellations are >> consecutively numbered, but there is no information about the >> anatomical >> location of these parcellations. >> >> In a first step, we would like to know which of the new parcellations >> are >> located within a particular brain structure (label), e.g. within the >> central >> sulcus as defined in the aparc.a2009s.annot. >> >> In a second step, we would like to extract the MNI coordinates of the >> centroids of these new parcellations. >> >> All suggestions are appreciated. >> >> Thanks in advance >> Best regards >> >> Diana >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_make_face_parcellation
Hi We were able to extract the vertex number (and MNI coordinates) for the finer parcellation as well as for the aparc.a2005s parcellation by using mri_annotation2label. Now we have a .label file for each parcellation where all vertices number (and their coordinates) that belong to a parcellation are listed. Do you have any suggestion or idea how to match the vertex number for both parcellations in order to get the anatomical labels for the finer parcellation? Kind regards Diana Am 14.04.2010 um 15:01 schrieb Bruce Fischl: > yes, you can use the talairach.xfm file to get MNI coords of > whatever you want. Not sure if it is reported anywhere by default > though. Doug? > On Wed, 14 Apr 2010, Diana Wotruba wrote: > >> Hi Bruce >> Thank you for the quick answer. We already considered using >> mris_divide_parcellation. Unfortunately the result is a strip shaped >> parcellation scheme, which is not suitable for our aim. Therefore we >> would rather use mris_make_face_parcellation. Is there no other way >> to >> get the MNI Coordinates of these vertices and the label corresponding >> to them? >> >> Thanks very much for your help! >> Kind regards >> Diana >> >> >> Am 12.04.2010 um 00:31 schrieb Bruce Fischl: >> >>> Hi Diana, >>> >>> the parcels from mris_make_face_parcellation are uniform, not >>> localized >>> to gyral/sulcal labels. If that is important try using >>> mris_divide_parcellation instead. >>> >>> cheers >>> Bruce >>> >>> >>> On Sun, 11 Apr 2010, Diana >>> Wotruba wrote: >>> >>>> Dear FS experts >>>> We used mris_make_face_parcellation to get a finer parcellation of >>>> the >>>> cortical surface. The labels of the resulting parcellations are >>>> consecutively numbered, but there is no information about the >>>> anatomical >>>> location of these parcellations. >>>> >>>> In a first step, we would like to know which of the new >>>> parcellations >>>> are >>>> located within a particular brain structure (label), e.g. within >>>> the >>>> central >>>> sulcus as defined in the aparc.a2009s.annot. >>>> >>>> In a second step, we would like to extract the MNI coordinates of >>>> the >>>> centroids of these new parcellations. >>>> >>>> All suggestions are appreciated. >>>> >>>> Thanks in advance >>>> Best regards >>>> >>>> Diana >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> ___ >>> Freesurfer mailing list >>> 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. >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
